Merge pull request #76 from cadenmyers13/new-scikit

sbillinge · web-flow · commit 1521c3379eba · 2025-01-06T18:04:45.000-05:00
fix: Update `.github/` and `.pre-commit-config.yaml`
diff --git a/.codecov.yml b/.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]
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -12,11 +12,11 @@ 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 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).
-- [ ] 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.
+- [ ] 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:
 
@@ -42,5 +42,5 @@ Please let @sbillinge know that all checks are done and the package is ready for
 
 <!-- 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.
diff --git a/.github/workflows/build-wheel-release-upload.yml b/.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
     with:
       project: diffpy.fourigui
+      c_extension: false
+      github_admin_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml
@@ -3,10 +3,10 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
-  build:
+  check-news-item:
     uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.fourigui
diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml
@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
+  matrix-coverage:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.fourigui
diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml
@@ -1,14 +1,10 @@
 name: Deploy Documentation on Release
 
 on:
-  release:
-    types: [published]
   workflow_dispatch:
 
 jobs:
   docs:
-    permissions:
-      contents: write
     uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
       project: diffpy.fourigui
diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  validate:
+  tests-on-pr:
     uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.fourigui
diff --git a/.pre-commit-config.yaml b/.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]
diff --git a/news/workflows.rst b/news/workflows.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Modify `.github` directory and `.pre-commit-config.yaml` to comply with renaming of package maintainer.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Blank namespace package for module diffpy."""
 
 
diff --git a/src/diffpy/fourigui/__init__.py b/src/diffpy/fourigui/__init__.py
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Tool for visualizing 3D diffraction and PDF Images."""
 
 # package version
diff --git a/src/diffpy/fourigui/fourigui.py b/src/diffpy/fourigui/fourigui.py
@@ -21,7 +21,7 @@ def __init__(self):
         self.initUI()
 
     def initUI(self):
-        """Initialize the GUI for fourigui"""
+        """Initialize the GUI for fourigui."""
 
         self.loaded = False  # denotes whether a dataset is loaded
         self.transformed = False  # denotes whether dataset is Fourier transformed
@@ -254,11 +254,10 @@ def initUI(self):
         frame11.place(x=WIDTH // 2, y=HEIGHT // 2)  # , 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")
@@ -327,7 +326,7 @@ def load_cube(self):
         self.intensity_upd_global()
 
     def plot_plane(self):
-        """update plotted plane perpendicular to the selected axis"""
+        """Update plotted plane perpendicular to the selected axis."""
         if self.axis.get() == 0:
             self.im.set_data(self.cube[self.plane_num.get(), :, :])
         elif self.axis.get() == 1:
@@ -339,7 +338,7 @@ def plot_plane(self):
         self.canvas.draw()
 
     def colorrange_upd(self):
-        """change color range in plot"""
+        """Change color range in plot."""
         try:
             if self.colorbarmin.get() and self.colorbarmax.get():
                 vmin = float(self.colorbarmin.get())
@@ -359,7 +358,8 @@ 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:
@@ -373,7 +373,7 @@ 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"] = f"{np.format_float_scientific(np.nanmax(self.cube), 1)}"
@@ -382,10 +382,8 @@ 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)
@@ -438,10 +436,9 @@ 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
@@ -455,8 +452,7 @@ def ifft(self):
         self.intensity_upd_global()
 
     def applycutoff(self):
-        """
-        shape the reciprocal-space array
+        """Shape the reciprocal-space array.
 
         reassign all voxels with distance smaller than qmin and greater than qmax
         to np.nan.
@@ -507,9 +503,8 @@ 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:
@@ -522,9 +517,8 @@ def redocutuff(self):
         self.intensity_upd_global()
 
     def newcutoff(self):
-        """
-        Apply a new cutoff based on the current space and cutoff settings.
-        """
+        """Apply a new cutoff based on the current space and cutoff
+        settings."""
         if self.cutoff.get():
             if self.space.get() and self.transformed:
                 self.cube = self.cube_real
@@ -535,9 +529,8 @@ 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
@@ -547,9 +540,7 @@ def plot_next_plane(self):
         self.plot_plane()
 
     def animation(self):
-        """
-        slices through the 3D array along the selected axis
-        """
+        """Slices through the 3D array along the selected axis."""
         try:
             if not self.anientry.get():
                 anispeed = 1
@@ -563,9 +554,7 @@ 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
 
diff --git a/src/diffpy/fourigui/version.py b/src/diffpy/fourigui/version.py
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Definition of __version__."""
 
 #  We do not use the other three variables, but can be added back if needed.
diff --git a/tests/test_version.py b/tests/test_version.py
@@ -1,10 +1,10 @@
-"""Unit tests for __version__.py
-"""
+"""Unit tests for __version__.py."""
 
 import diffpy.fourigui
 
 
 def test_package_version():
-    """Ensure the package version is defined and not set to the initial placeholder."""
+    """Ensure the package version is defined and not set to the initial
+    placeholder."""
     assert hasattr(diffpy.fourigui, "__version__")
     assert diffpy.fourigui.__version__ != "0.0.0"

Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,6 @@`
`12`	`12`	`# See LICENSE.rst for license information.`
`13`	`13`	`#`
`14`	`14`	`##############################################################################`
`15`		`-`
`16`	`15`	`"""Blank namespace package for module diffpy."""`
`17`	`16`
`18`	`17`