chore: re-scikit-packaged diffpy.srmise

Author: stevenhua0320

.flake8

@@ -6,7 +6,7 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
+    docs/source/conf.py
 max-line-length = 115
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -11,12 +11,13 @@ assignees: ""
 - [ ] All PRs/issues attached to the release are merged.
 - [ ] 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.
+- [ ] Locally rendered documentation contains all appropriate pages, tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally.
 - [ ] Installation instructions in the README, documentation, and the website are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
 - [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release.
+- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`.
 
 Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 
@@ -34,7 +35,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 

.github/workflows/build-and-publish-docs-on-dispatch.yml

@@ -0,0 +1,18 @@
+name: Build and Publish Docs on Dispatch
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-python-version:
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+    with:
+      python_version: 0
+
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: diffpy.srmise
+      c_extension: false
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

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

@@ -1,18 +1,76 @@
-name: Release (GitHub/PyPI) and Deploy Docs
+name: Build Wheel and Release
 
+# Trigger on tag push or manual dispatch.
+# Tag and release privilege are verified inside the reusable workflow.
 on:
   workflow_dispatch:
   push:
     tags:
-      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*"
+
+# ── Release modality ──────────────────────────────────────────────────────────
+# Three options are provided below. Only ONE job should be active at a time.
+# To switch: comment out the active job and uncomment your preferred option,
+# then commit the change to main before tagging a release.
+# ─────────────────────────────────────────────────────────────────────────────
 
 jobs:
-  release:
+  # Option 1 (default): Release to GitHub, publish to PyPI, and deploy docs.
+  #
+  # The wheel is uploaded to PyPI so users can install with `pip install`.
+  # A GitHub release is created with the changelog as the release body, and
+  # the Sphinx documentation is rebuilt and deployed to GitHub Pages.
+  #
+  # Choose this for open-source packages distributed via PyPI and/or
+  # conda-forge where broad public availability is the goal.
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.srmise
       c_extension: false
-      maintainer_GITHUB_username: sbillinge
+      maintainer_github_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Option 2: Release to GitHub and deploy docs, without publishing to PyPI.
+  #
+  # A GitHub release is created and the Sphinx docs are deployed, but the
+  # wheel is not uploaded to PyPI. The source code remains publicly visible
+  # on GitHub and can be installed directly from there.
+  #
+  # Choose this when the package is public but you prefer to keep it off the
+  # default pip index — for example, if you distribute via conda-forge only,
+  # or if the package is not yet ready for a permanent PyPI presence.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-no-pypi:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-no-pypi.yml@v0
+  #   with:
+  #     project: diffpy.srmise
+  #     c_extension: false
+  #     maintainer_github_username: sbillinge, Ainamacar
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Option 3: Release to GitHub with wheel, license, and instructions bundled
+  # as a downloadable zip attached to the GitHub release asset.
+  #
+  # The wheel is built and packaged together with INSTRUCTIONS.txt and the
+  # LICENSE file into a zip that is attached directly to the GitHub release.
+  # Users with access to the (private) repo download the zip, follow the
+  # instructions inside, and install locally with pip. No PyPI or conda-forge
+  # upload occurs, and no docs are deployed.
+  #
+  # Choose this for private or restricted packages where distribution must be
+  # controlled: only users with repo access can download the release asset,
+  # making the GitHub release itself the distribution channel.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-private:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-private-pure.yml@v0
+  #   with:
+  #     project: diffpy.srmise
+  #     maintainer_github_username: sbillinge, Ainamacar
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-      - main
+      - main # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
 
 jobs:
   check-news-item:

.github/workflows/matrix-and-codecov.yml

@@ -0,0 +1,21 @@
+name: Matrix and Codecov
+
+on:
+  # push:
+  #   branches:
+  #     - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+jobs:
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.srmise
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

AUTHORS.rst

@@ -1,8 +1,7 @@
 Authors
 =======
 
-Luke Granlund
-Billinge Group and community contributors.
+Luke Granlund, Simon Billinge, Billinge Group members
 
 Contributors
 ------------

CODE_OF_CONDUCT.rst CODE-OF-CONDUCT.rstCODE_OF_CONDUCT.rst renamed to CODE-OF-CONDUCT.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.srmise
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -25,8 +25,9 @@
         :target: https://anaconda.org/conda-forge/diffpy.srmise
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srmise/pulls
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.srmise
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srmise
         :target: https://pypi.org/project/diffpy.srmise/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.srmise
@@ -35,54 +36,18 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.srmise/issues
 
-Implementation of the ParSCAPE algorithm for peak extraction from atomic pair distribution functions (PDFs)
-
-SrMise is an implementation of the `ParSCAPE algorithm
-<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
-atomic pair distribution functions (PDFs).  It is designed to function even
-when *a priori* knowledge of the physical sample is limited, utilizing the
-Akaike Information Criterion (AIC) to estimate whether peaks are
-statistically justified relative to alternate models.  Three basic use cases
-are anticipated for SrMise.  The first is peak fitting a user-supplied
-collections of peaks.  The second is peak extraction from a PDF with no (or
-only partial) user-supplied peaks.  The third is an AIC-driven multimodeling
-analysis where the output of multiple SrMise trials are ranked.
-
-The framework for peak extraction defines peak-like clusters within the data,
-extracts a single peak within each cluster, and iteratively combines nearby
-clusters while performing a recursive search on the residual to identify
-occluded peaks.  Eventually this results in a single global cluster
-containing many peaks fit over all the data.  Over- and underfitting are
-discouraged by use of the AIC when adding or, during a pruning step, removing
-peaks.  Termination effects, which can lead to physically spurious peaks in
-the PDF, are incorporated in the mathematical peak model and the pruning step
-attempts to remove peaks which are fit better as termination ripples due to
-another peak.
-
-Where possible, SrMise provides physically reasonable default values
-for extraction parameters.  However, the PDF baseline should be estimated by
-the user before extraction, or by performing provisional peak extraction with
-varying baseline parameters.  The package defines a linear (crystalline)
-baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline,
-and an arbitrary baseline interpolated from a list of user-supplied values.
-In addition, PDFs with accurate experimentally-determined uncertainties are
-necessary to provide the most reliable results, but historically such PDFs
-are rare.  In the absence of accurate uncertainties an *ad hoc* uncertainty
-must be specified.
+Peak extraction and peak fitting tool for atomic pair distribution functions.
+
+* LONGER DESCRIPTION HERE
 
 For more information about the diffpy.srmise library, please consult our `online documentation <https://diffpy.github.io/diffpy.srmise>`_.
 
 Citation
 --------
 
-If you use this program for a scientific research that leads
-to publication, we ask that you acknowledge use of the program
-by citing the following paper in your publication:
+If you use diffpy.srmise in a scientific publication, we would like you to cite this package as
 
-   L. Granlund, S. J. L. Billinge and P. M. Duxbury,
-   `Algorithm for systematic peak extraction from atomic pair distribution functions
-   <http://dx.doi.org/10.1107/S2053273315005276>`__,
-   *Acta Crystallogr. A* **4**, 392-409 (2015).
+        diffpy.srmise Package, https://github.com/diffpy/diffpy.srmise
 
 Installation
 ------------
@@ -101,10 +66,6 @@ The following creates and activates a new environment named ``diffpy.srmise_env`
         conda create -n diffpy.srmise_env diffpy.srmise
         conda activate diffpy.srmise_env
 
-To confirm that the installation was successful, type ::
-
-        python -c "import diffpy.srmise; print(diffpy.srmise.__version__)"
-
 The output should print the latest version displayed on the badges above.
 
 If the above does not work, you can use ``pip`` to download and install the latest release from
@@ -119,6 +80,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.srmise --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.srmise; print(diffpy.srmise.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.srmise -h
+
 Getting Started
 ---------------
 
@@ -127,9 +101,7 @@ You may consult our `online documentation <https://diffpy.github.io/diffpy.srmis
 Support and Contribute
 ----------------------
 
-`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.srmise. Please join the diffpy.srmise users community by joining the Google group. The diffpy.srmise project welcomes your expertise and enthusiasm!
-
-If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srmise/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srmise/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srmise/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srmise/pulls>`_.
 
 Feel free to fork the project and contribute. To install diffpy.srmise
 in a development mode, with its sources being directly used by Python
@@ -152,9 +124,14 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srmise/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srmise/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Contact
 -------
 
-For more information on diffpy.srmise please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.srmise please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.srmise`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.