Merge pull request #82 from tinatn29/setup-CI-redo

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

Author: sbillinge

.codespell/ignore_words.txt

@@ -4,11 +4,5 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
-
-;; cutted used as attribute in unit_test.py and fourigui.py
-cutted

.gitattributes

@@ -13,30 +13,30 @@ assignees: ""
 - [ ] 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.
-- [ ] Installation instructions in the README, documentation, and the website (e.g., diffpy.org) are updated.
+- [ ] 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.
 
-Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+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:
 
 ### PyPI/GitHub full-release preparation checklist:
 
 - [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
 - [ ] License information on PyPI is correct.
-- [ ] Docs are deployed successfully to `https://www.diffpy.org/<package-name>`.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
 - [ ] Successfully run all tests, tutorial examples or do functional testing.
 
-Please let @sbillinge know that all checks are done and the package is ready for full release.
+Please let the maintainer know that all checks are done and the package is ready for full release.
 
 ### conda-forge release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+<!-- 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.
-- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have questions.
-- [ ] Tag @sbillinge and @bobleesj for conda-forge release.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
 
 ### Post-release checklist
 

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,15 @@
+### What problem does this PR address?
+
+<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
+
+### What should the reviewer(s) do?
+
+<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
+
+<!--
+Use the following checklist items when applicable (select only what applies):
+- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
+    - [ ] Documentation (e.g., tutorials, examples, README) has been updated.
+    - [ ] A tracking issue or plan to update documentation exists.
+- [ ] This PR affects internal functionality only (no user-facing change).
+-->

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -8,11 +8,11 @@ on:
 
 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.fourigui
       c_extension: false
-      github_admin_username: sbillinge
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -7,6 +7,6 @@ on:
 
 jobs:
   check-news-item:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.fourigui

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

@@ -12,7 +12,7 @@ on:
 
 jobs:
   matrix-coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.fourigui
       c_extension: false

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

@@ -5,7 +5,7 @@ on:
 
 jobs:
   docs:
-    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
       project: diffpy.fourigui
       c_extension: false

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

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

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

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/

.gitignore

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "latest"
+
+python:
+  install:
+    - requirements: requirements/docs.txt
+
+sphinx:
+  configuration: doc/source/conf.py

.readthedocs.yaml

@@ -1,5 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments

CHANGELOG.rst

@@ -8,7 +8,7 @@ Our Pledge
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

CODE_OF_CONDUCT.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.fourigui
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -26,7 +26,7 @@
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.fourigui
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.fourigui
         :target: https://pypi.org/project/diffpy.fourigui/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.fourigui
@@ -129,4 +129,9 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.fourigui please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.fourigui please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at [email protected].
+
+Acknowledgements
+----------------
+
+``diffpy.fourigui`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

README.rst

@@ -59,6 +59,11 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
 line-length = 79
 include = '\.pyi?$'

requirements/build.txt renamed to doc/source/img/.placeholder

@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r

doc/source/snippets/.placeholder

@@ -15,7 +15,7 @@
 """Tool for visualizing 3D diffraction and PDF images."""
 
 # package version
-from diffpy.fourigui.version import __version__
+from diffpy.fourigui.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True

environment.yml

@@ -285,10 +285,10 @@ def initUI(self):
         )  # , height=HEIGHT//2, width=WIDTH//2)
 
     def load_cube(self):
-        """Loads 3D array in h5py file format from the filename input panel 3D
-        array is expected to be a reconstructed reciprocal scattering volume
-        when executed, one slide perpendicular to the selected axis will be
-        plotted in the plot panel."""
+        """Loads 3D array in h5py file format from the filename input
+        panel 3D array is expected to be a reconstructed reciprocal
+        scattering volume when executed, one slide perpendicular to the
+        selected axis will be plotted in the plot panel."""
 
         filename = self.filename_entry.get()
         f = h5py.File(filename, "r")
@@ -397,8 +397,8 @@ def colorrange_upd(self):
         self.plot_plane()
 
     def intensity_upd_local(self):
-        """Show local intensity minimum, maximum and sum of current plotted
-        plane."""
+        """Show local intensity minimum, maximum and sum of current
+        plotted plane."""
         if self.axis.get() == 0:
             plane = self.cube[self.plane_num.get(), :, :]
         elif self.axis.get() == 1:
@@ -418,7 +418,8 @@ def intensity_upd_local(self):
         self.localnanratio["text"] = f"{round(nan_ratio, 2)}"
 
     def intensity_upd_global(self):
-        """Load global intensity minimum, maximum and sum of 3D array."""
+        """Load global intensity minimum, maximum and sum of 3D
+        array."""
         self.intensity_upd_local()
         nan_ratio = np.count_nonzero(np.isnan(self.cube)) / self.cube.size
         self.globalmax["text"] = (
@@ -433,8 +434,9 @@ def intensity_upd_global(self):
         self.globalnanratio["text"] = "{}".format(round(nan_ratio, 2))
 
     def fft(self):
-        """Fourier transform 3D array from reciprocal to real space the origin
-        of reciprocal and real space is expected to be the central voxel."""
+        """Fourier transform 3D array from reciprocal to real space the
+        origin of reciprocal and real space is expected to be the
+        central voxel."""
 
         def perform_fft(fftholder):
             fftholder = np.nan_to_num(fftholder)
@@ -487,9 +489,9 @@ def perform_fft(fftholder):
         self.intensity_upd_global()
 
     def ifft(self):
-        """Inverse Fourier transform 3D array from real to reciprocal space the
-        origin of real and reciprocal space is expected to be the central
-        voxel."""
+        """Inverse Fourier transform 3D array from real to reciprocal
+        space the origin of real and reciprocal space is expected to be
+        the central voxel."""
         if not self.cutoff.get():
             self.cube_real = self.cube
             self.cube = self.cube_reci
@@ -562,8 +564,8 @@ def applycutoff(self):
             self.intensity_upd_global()
 
     def redocutuff(self):
-        """Redo the cutoff operation depending on the current space (real or
-        reciprocal)."""
+        """Redo the cutoff operation depending on the current space
+        (real or reciprocal)."""
         if self.space.get():  # in real space
             self.cube_realcut = self.cube
             if not self.transformed:
@@ -588,8 +590,8 @@ def newcutoff(self):
         self.applycutoff()
 
     def plot_next_plane(self):
-        """Plot the next plane in the dataset, looping back to the first if at
-        the end."""
+        """Plot the next plane in the dataset, looping back to the first
+        if at the end."""
         n = self.plane_num.get()
         if n == len(self.cube[self.axis.get()]) - 1:
             n = 0
@@ -616,7 +618,8 @@ def animation(self):
         self.plot_next_plane()
 
     def multiple_funcs(*funcs):
-        """Executes multiple functions passed as arguments in sequence."""
+        """Executes multiple functions passed as arguments in
+        sequence."""
         for func in funcs:
             func
 

pyproject.toml

@@ -7,7 +7,7 @@
 # File coded by: Billinge Group members and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.fourigui/graphs/contributors
+# https://github.com/diffpy/diffpy.fourigui/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #

requirements/docs.txt

@@ -1,6 +1,6 @@
 """Unit tests for __version__.py."""
 
-import diffpy.fourigui
+import diffpy.fourigui  # noqa
 
 
 def test_package_version():