Merge pull request #132 from Sparks29032/cookie

Cookie Cutter + PyPi fix

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

@@ -0,0 +1,12 @@
+name: Check for News
+
+on:
+  pull_request_target:
+    branches:
+    - main
+
+jobs:
+  build:
+    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    with:
+      project: diffpy.pdfmorph

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

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

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

@@ -0,0 +1,14 @@
+name: Build and Deploy Docs
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.pdfmorph
+      c_extension: false

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

@@ -0,0 +1,16 @@
+name: Tests on PR
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  validate:
+    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    with:
+      project: diffpy.pdfmorph
+      c_extension: false
+      headless: false

.pre-commit-config.yaml

@@ -16,7 +16,10 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: '\.(rst|txt)$'
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-added-large-files
   - repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contibutors.
+Billinge Group and community contributors.
 
 Contributors
 ------------

MANIFEST.in

@@ -1,15 +1,12 @@
-include AUTHORS.rst
-include LICENSE
-include README.rst
-include requirements.txt
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat
-
-include versioneer.py
-include diffpy.pdfmorph/_version.py
-
-# If including data files in the package, add them like:
-# include path/to/data_file
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.

README.rst

@@ -75,8 +75,8 @@ REQUIREMENTS
 ------------------------------------------------------------------------
 
 PDFmorph is currently run from the command line, which requires opening
-and typing into a terminal window or Windows command prompt. It is 
-recommended that you consult online resources and become somewhat 
+and typing into a terminal window or Windows command prompt. It is
+recommended that you consult online resources and become somewhat
 familiar before using PDFmorph.
 
 PDFmorph can be run with Python 3.10 or higher. It makes use of several third party
@@ -115,7 +115,7 @@ Another option is to use ``pip`` to download and install the latest release from
 `Python Package Index <https://pypi.python.org>`_.
 To install using ``pip`` into your ``diffpy.pdfmorph_env`` environment, we will also have to install dependencies ::
 
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/run.txt
+        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/pip.txt
 
 and then install the package ::
 
@@ -160,7 +160,7 @@ 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.pdfmorph. Please join the diffpy.pdfmorph users community by joining the Google group. The diffpy.pdfmorph 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.pdfmorph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfmorph/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.pdfmorph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfmorph/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
 
 Feel free to fork the project and contribute. To install diffpy.pdfmorph
 in a development mode, with its sources being directly used by Python

TUTORIAL.rst

@@ -183,5 +183,5 @@ Enjoy the software!
 Bug Reports
 -----------
 
-Please enjoy using our software! If you come accross any bugs in the 
+Please enjoy using our software! If you come accross any bugs in the
 application, please report them to [email protected]

doc/make.bat

@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PackagingScientificPython
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd