Re-cookiecut: implement codecov, install pdffit2 rc, limit to py3.12

.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]

.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.

.codespell/ignore_words.txt

@@ -0,0 +1,20 @@
+;; 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
+
+;; abbreviation for "structure"
+struc
+
+;; method name within JournalPanel class
+onText
+
+;; a method name within JournalPanel class
+delt

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -6,17 +6,41 @@ labels: "release"
 assignees: ""
 ---
 
-### Release checklist for GitHub contributors
+### PyPI/GitHub rc-release preparation checklist:
 
 - [ ] 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.
-- [ ] 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.
-- [ ] 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.
+  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.
+
+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:
+
+### 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>`.
+- [ ] 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.
+
+### conda-forge release preparation checklist:
+
+<!-- After @sbillinge 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.
+
+### 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. 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

@@ -1,4 +1,4 @@
-name: Release (GitHub/PyPI)
+name: Release (GitHub/PyPI) and Deploy Docs
 
 on:
   workflow_dispatch:

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

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

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

@@ -12,10 +12,61 @@ on:
 
 jobs:
   coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
-    with:
-      project: diffpy.pdfgui
-      c_extension: false
-      headless: true
-    secrets:
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        python-version: ["3.11", "3.12"]
+    env:
+          LATEST_PYTHON_VERSION: "3.12"
+    steps:
+      - name: Check out diffpy.pdfgui
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.pdfgui and requirements
+        run: |
+          conda install --file requirements/test.txt
+          conda install wxpython diffpy.utils matplotlib-base
+          pip install diffpy.pdffit2==1.4.4rc6
+          python -m pip install . --no-deps
+
+      - name: Start Xvfb for ubuntu-latest only
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get install -y xvfb
+          export DISPLAY=:99
+          Xvfb :99 -screen 0 1024x768x16 &
+
+      - name: Validate diffpy.pdfgui
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+            export DISPLAY=:99
+          fi
+          pytest --cov
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == env.LATEST_PYTHON_VERSION
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -1,9 +1,8 @@
-name: Build and Deploy Docs
+name: Deploy Documentation on Release
 
 on:
   release:
-    types:
-      - published
+    types: [published]
   workflow_dispatch:
 
 jobs:
@@ -12,3 +11,5 @@ jobs:
     with:
       project: diffpy.pdfgui
       c_extension: false
+      headless: true
+      python_version: 3.12

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

@@ -9,8 +9,52 @@ on:
 
 jobs:
   validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
-    with:
-      project: diffpy.pdfgui
-      c_extension: false
-      headless: true
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.pdfgui
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+          python-version: 3.12
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.pdfgui and requirements
+        run: |
+          conda install --file requirements/test.txt
+          conda install wxpython diffpy.utils matplotlib-base
+          pip install diffpy.pdffit2==1.4.4rc6
+          python -m pip install . --no-deps
+
+      - name: Start Xvfb
+        run: |
+          sudo apt-get install -y xvfb
+          export DISPLAY=:99
+          Xvfb :99 -screen 0 1024x768x16 &
+
+      - name: Validate diffpy.pdfgui
+        run: |
+          export DISPLAY=:99
+          pytest --cov
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          verbose: true
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.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

README.rst

@@ -132,7 +132,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfgui/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfgui/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------

doc/manual/html/readme.txt

@@ -1,2 +1,2 @@
-This directory need to be relativly the same as doc/build/html/manual from
+This directory need to be relatively the same as doc/build/html/manual from
 doc/source/_static/images

doc/manual/pdfgui.texinfo

@@ -243,7 +243,7 @@ requirements. This can be done either for all atoms in the structure or for an
 arbitrary subset - for example when it is known that only a certain species
 show a local distortion. The code for space group definitions was provided by
 the Python Macromolecular Library (mmLib,
-@url{http://pymmlib.sourceforge.net}).  This was extened to include
+@url{http://pymmlib.sourceforge.net}).  This was extended to include
 non-standard space groups using the Computational Crystallography Toolbox
 (cctbx, @uref{https://cctbx.github.io}).  PDFgui also supports supercell
 expansion of a normal unit cell.

news/codecov.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* Codecov coverage report in PRs
+* Spelling check with Codespell in pre-commit
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "GUI for PDF simulation and structure refinement."
 keywords = ['PDF structure refinement GUI']
 readme = "README.rst"
-requires-python = ">=3.10"
+requires-python = ">=3.11, <3.13"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,7 +25,6 @@ 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',
         'Topic :: Scientific/Engineering :: Physics',
@@ -54,6 +53,11 @@ 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,*.html,*.m,*.textinfo"
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

src/diffpy/pdfgui/control/calculation.py

@@ -252,7 +252,7 @@ def load(self, z, subpath):
         z       -- zipped project file
         subpath -- path to its own storage within project file
 
-        returns a tree of internal hierachy
+        returns a tree of internal hierarchy
         """
         config = pickle.loads(z.read(subpath + "config"), encoding="latin1")
         self.rmin = config["rmin"]

src/diffpy/pdfgui/control/fitstructure.py

@@ -35,7 +35,7 @@ class FitStructure(PDFStructure):
     Class data members:
         symposeps   -- tolerance for recognizing site as symmetry position
 
-    Data members (in adition to those in PDFStructure):
+    Data members (in addition to those in PDFStructure):
         owner       -- instance of parent Fitting (set in Organizer.add())
         initial     -- initial structure, same as self
         refined     -- refined structure when available or None