Merge branch 'main' into gt2

sbillinge · web-flow · commit 59c555123195 · 2024-11-09T01:19:32.000-05:00
diff --git a/.codecov.yml b/.codecov.yml
@@ -1,34 +1,14 @@
-# codecov can find this file anywhere in the repo, so we don't need to clutter
-# the root folder.
-#comment: false
-
-codecov:
-  notify:
-    require_ci_to_pass: no
-
 coverage:
   status:
-    patch:
+    project:  # more options at https://docs.codecov.com/docs/commit-status
       default:
-        target: '70'
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: failure
-    project:
-      default: false
-      library:
-        target: auto
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: error
-        paths: '!*/tests/.*'
-
-      tests:
-        target: 97.9%
-        paths: '*/tests/.*'
-        if_not_found: success
-
-flags:
-  tests:
-    paths:
-      - tests/
+        target: auto # use the coverage from the base commit, fail if coverage is lower
+        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]
+  hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]
diff --git a/.codespell/ignore_lines.txt b/.codespell/ignore_lines.txt
@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.
diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt
@@ -0,0 +1,14 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; 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
diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -13,10 +13,16 @@ 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 on the website (e.g., diffpy.org) are updated and
-  tested
-- [ ] Successfully run any tutorial examples or do functional testing in some other way.
+- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version
 - [ ] Grammar and writing quality have been checked (no typos).
 
 Please mention @sbillinge when you are ready for release. Include any additional comments necessary, such as
-version information and details about the pre-release.
+version information and details about the pre-release here:
+
+### Post-release checklist
+
+Before closing this issue, please complete the following:
+
+- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README.
+- [ ]  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
@@ -1,4 +1,4 @@
-name: Release (GitHub/PyPI)
+name: Release (GitHub/PyPI) and Deploy Docs
 
 on:
   workflow_dispatch:
diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
@@ -14,3 +14,5 @@ jobs:
       project: diffpy.fourigui
       c_extension: false
       headless: true
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -44,3 +44,9 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli
diff --git a/README.rst b/README.rst
@@ -56,7 +56,6 @@ If you use diffpy.fourigui in a scientific publication, we would like you to cit
         `Real-Space Texture and Pole-Figure Analysis Using the 3D Pair Distribution
         Function on a Platinum Thin Film <https://doi.org/10.1107/S2052252522006674>`_. *IUCrJ* **9 (5)**, 594–603 (2022).
 
-
 Installation
 ------------
 
@@ -125,7 +124,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.fourigui/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.fourigui/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------
diff --git a/news/codespell.rst b/news/codespell.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Added `codespell` for spell check on all files.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/news/numpy_dep.rst b/news/numpy_dep.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed deprecation warning presented by numpy2
+
+**Security:**
+
+* <news item>
diff --git a/news/pythonversion.rst b/news/pythonversion.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Removed support for python `<3.11`
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/news/test.rst b/news/test.rst
@@ -16,7 +16,7 @@
 
 **Fixed:**
 
-* Surpress `RuntimeWarning` in tests for the `applycutoff` function
+* Suppress the `RuntimeWarning` in tests for the `applycutoff` function
 
 **Security:**
 
diff --git a/news/tutorialdoc.rst b/news/tutorialdoc.rst
@@ -1,6 +1,6 @@
 **Added:**
 
-* Add tutorial to API
+* Add tutorial to documentation
 
 **Changed:**
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,7 +14,7 @@ maintainers = [
 description = "Tool for visualizing 3D diffraction and PDF Images."
 keywords = ['diffraction', 'pdf', 'pair distribution function', 'gui']
 readme = "README.rst"
-requires-python = ">=3.10, <3.14"
+requires-python = ">=3.11, <3.14"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,9 +25,9 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
@@ -54,6 +54,11 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif,*.dat"
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'
diff --git a/src/diffpy/fourigui/fourigui.py b/src/diffpy/fourigui/fourigui.py
@@ -155,10 +155,10 @@ def initUI(self):
         anibutton.grid(row=8, column=4)
 
         # row 10-12 Fourier transformation
-        seperator = tk.Label(
+        separator = tk.Label(
             frame00, text=" "
         )  # __________________________________________________________________")
-        seperator.grid(row=9, column=0, columnspan=5)
+        separator.grid(row=9, column=0, columnspan=5)
         cutofflabel = tk.Label(frame00, text="cutoff frequency")
         cutofflabel.grid(row=10, column=2, columnspan=2)
         qminlabel = tk.Label(frame00, text="qmin [px]:")
@@ -390,8 +390,9 @@ def fft(self):
         def perform_fft(fftholder):
             fftholder = np.nan_to_num(fftholder)
             size = list(fftholder.shape)
+            axes = list(range(fftholder.ndim))
             fftholder = np.fft.ifftshift(fftholder)
-            fftholder = np.fft.fftn(fftholder, s=size, norm="ortho")
+            fftholder = np.fft.fftn(fftholder, s=size, axes=axes, norm="ortho")
             fftholder = np.fft.fftshift(fftholder)
             fftholder = fftholder.real
             return fftholder
diff --git a/tests/integration_test.py b/tests/integration_test.py
@@ -97,6 +97,19 @@ def test_fft_testdataset3(self):
         # then
         self.assertTrue(np.allclose(result, self.test_gofr_cut_15to35px))
 
+        # Desired behavior is nans in the arrays below qmin and above qmax.  As a result, np.nanmax will generate
+        # runtimewarnings when it # encounters slices that are all nans. capture these so tests pass cleanly
+        # without warnings
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=RuntimeWarning)
+            # when
+            self.test_gui.applycutoff()
+        result = self.test_gui.cube
+
+        # then
+        # with self.assertWarns(RuntimeWarning):
+        self.assertTrue(np.allclose(np.nan_to_num(result), np.nan_to_num(self.test_sofq_cut_15to35px)))
+
 
 if __name__ == "__main__":
     unittest.main()

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+;; Please include filenames and explanations for each ignored line.`
	`2`	`+;; See https://docs.openverse.org/meta/codespell.html for docs.`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Release (GitHub/PyPI)`
	`1`	`+name: Release (GitHub/PyPI) and Deploy Docs`
`2`	`2`
`3`	`3`	`on:`
`4`	`4`	`workflow_dispatch:`