Merge pull request #4 from xraysoftmat/main

Merge main to dev

Author: mattgebert

.gitignore

@@ -162,5 +162,5 @@ cython_debug/
 # Datafiles
 .asc
 
-test*
+tests/archive*
 .vscode*

.pre-commit-config.yaml

@@ -1,18 +1,37 @@
+## `Pre-commit` module configuration file
+## Can be installed using `pip install pre-commit`
+## The pre-commit hooks can then be installed using `pre-commit install`
+## All checks are run by default when `git commit` is run.
+
 repos:
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  -   id: black
+# Pre-commit hooks for basic Python processing
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
+
+# Black - for standard code formatting
+-   repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+    -   id: black
 
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
-  hooks:
-  -   id: trailing-whitespace
-  -   id: end-of-file-fixer
-  -   id: check-yaml
-  -   id: check-added-large-files
+# NumPyDoc - for docstring validation
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+      - id: numpydoc-validation
 
-# - repo: https://github.com/numpy/numpydoc
-#   rev: v1.6.0
-#   hooks:
-#     - id: numpydoc-validation
+# Python Semantic Release & commitizen - for automatic versioning
+-   repo: https://github.com/commitizen-tools/commitizen
+    rev: v4.1.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+      - id: commitizen-branch
+        stages: [pre-push]

pyNexafs/__main__.py

@@ -0,0 +1,22 @@
+"""
+Main entry point for the pyNexafs package.
+
+Runs the GUI for the package if the dependencies are met.
+Can be run from the command line with the command `python -m pyNexafs`.
+"""
+
+if __name__ == "__main__":
+    # Check if the dependencies are met
+    try:
+        import PyQt6
+    except ImportError as e:
+        print(
+            "PyQt6 is not installed. Please install PyQt6 to run the GUI."
+            + f"\nTraceback: {e}"
+        )
+        exit()
+
+    from pyNexafs.gui.data_browser import gui
+
+    # Create and run the app
+    gui()

pyproject.toml

@@ -1,58 +1,77 @@
+## What system to build the project with? I.e. Setuptools, Wheel, Poetry, etc.
+## Using `setuptools` here.
+
 [build-system]
-requires = [
-    "setuptools>=60",
-    "setuptools-scm>=8.0"
-]
-build-backend = "setuptools.build_meta"
+    requires = [
+        "setuptools>=60",
+        "setuptools-scm>=8.0"
+    ]
+    build-backend = "setuptools.build_meta"
 
 [project]
-name = "pyNexafs"
-# https://packaging.python.org/en/latest/specifications/version-specifiers/#version-specifiers
-# Use Major.Minor.Micro versioning.
-# version = "0.1.0"
-# https://pypi.org/project/setuptools-scm/ Generate a dynamic version based on .git information.
-dynamic = ["version"]
-dependencies = [
-    "scipy",
-    "numpy",
-    "pandas",
-    "overrides",
-    "xdrlib3" # for reading binary mda files
-]
-description = "A package for processing and analyzing NEXAFS data."
-license = {file = "LICENSE"}
-authors = [
-    {name = "Matthew Gebert", email="[email protected]"},
-    ]
-maintainers = [
-    {name = "Matthew Gebert", email="[email protected]"},
-]
-readme = "README.md"
-keywords = ["NEXAFS", "XAS", "synchrotron"]
-
-[tool.setuptools.packages.find] # All the following settings are optional:
-where = ["."]  # Root directory
-include = ["pyNexafs*"]
-exclude = []
+    # Project information
+    name = "pyNexafs"
+    version = "0.1.0"
+    description = "A package for processing and analysing NEXAFS data."
+    readme = "README.md"
+    license = {file = "LICENSE"}
+    keywords = ["NEXAFS", "XANES", "Near", "Edge", "X-ray", "Absorption", "Fine", "Structure", "Spectroscopy", "Optical Data", "XAS", "Synchrotron"]
+    authors = [
+        {name = "Matthew Gebert", email="[email protected]"},
+        ]
+    maintainers = [
+        {name = "Matthew Gebert", email="[email protected]"},
+    ]
+
+    # Project compatibility:
+    requires-python = ">=3.10"
+    dependencies = [
+        "numpy",
+        "overrides", # for type hinting
+        "scipy",
+        "xdrlib3" # function bindings for reading binary data from mda files
+    ]
+
+[project.urls]
+    # Website, documentation and other continuous integration URLS.
+    code = "https://github.com/mattgebert/pyNexafs"
+    documentation = "https://pyNexafs.readthedocs.io/en/latest/"
+
+[project.optional-dependencies]
+    gui = [
+        "matplotlib",
+        "pandas",
+        "pyqt6",
+        "pyyaml",
+    ]
+    dev = [
+        "commitizen",
+        "numpydoc",
+        "pre-commit",
+        "pytest",
+        "python-semantic-release",
+        "sphinx",
+        "sphinx-rtd-theme",
+    ]
+    docs = [
+        "sphinx",
+        "sphinx-rtd-theme",
+        "numpydoc",
+    ]
+
+# [tool.setuptools.packages.find] # All the following settings are optional:
+#     where = ["."]  # Root directory
+#     include = ["pyNexafs*"]
+#     exclude = []
 
 [tool.numpydoc_validation]
-checks = [
-    "all",   # report on all checks, except the below
-    "EX01",
-    "SA01",
-    "ES01",
-]
-
-# namespaces = true  # true by default
-
-### Example dependency usage
-# example <= 0.4
-# allowed operators <, >, <=, >=, == or !=,
-
-### Example inlcude
-# ["*"] by default
-
-### Example exclude
-# [] by default
-# "pyNexafs.tests*",
-# "pyNexafs.test_data*,
+    checks = [
+        "all",   # report on all checks, except the below
+        "EX01",
+        "SA01",
+        "ES01",
+    ]
+
+    exclude = [
+        'tests*',
+    ]