root, req

sbillinge · Oct 2, 2024 · Oct 2, 2024 · Oct 2, 2024 · Oct 2, 2024 · Oct 2, 2024
commit ec4462e1186b96060185e8834ab3b0e8ae7bd8c4
diff --git a/.pre-commit-config.yaml b/.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:

diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contibutors.
+Billinge Group and community contributors.
 
 Contributors
 ------------

diff --git a/MANIFEST.in b/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.
diff --git a/doc/make.bat b/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
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "diffpy.pdfmorph"
-dynamic=['version']
+dynamic=['version', 'dependencies']
 authors = [
   { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
 ]
@@ -37,10 +37,7 @@ pdfmorph = "diffpy.pdfmorph.pdfmorphapp:main"
 
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.pdfmorph/"
-Issues = "https://github.com/diffpy/diffpy.pdfmorph/issues"
-
-[tool.pytest.ini_options]
-pythonpath = ["src"]
+Issues = "https://github.com/diffpy/diffpy.pdfmorph/issues/"
 
 [tool.setuptools-git-versioning]
 enabled = true
@@ -51,9 +48,12 @@ dirty_template = "{tag}"
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
-exclude = ["diffpy.pdfmorph.tests*"]  # exclude packages matching these glob patterns (empty by default)
+exclude = ["tests"]  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements/run.txt"]}
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

diff --git a/requirements/README.txt b/requirements/README.txt
@@ -0,0 +1,11 @@
+# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES!
+#
+# This directory is where you should place your project dependencies.
+# "pip.txt" should contain all required packages not available on conda.
+# All other files should contain only packages available to download from conda. 
+# build.txt should contain all packages required to build (not run) the project.
+# run.txt should contain all packages (including optional packages) required for a user to run the program.
+# test.txt should contain all packages required for the testing suite and to ensure all tests pass.
+# docs.txt should contain all packages required for building the package documentation page.
+#
+# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES!
diff --git a/requirements/run.txt b/requirements/run.txt
@@ -1,5 +1,5 @@
 numpy
 scipy
 diffpy.utils
-matplotlib-base
+matplotlib
 bg-mpl-stylesheets