pyCHX upgrade with pixi

.gitattributes

@@ -1 +1,3 @@
 pyCHX/_version.py export-subst
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/docs.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v3
         with:
-          fetch-depth: 1000  # should be enough to reach the most recent tag
+          fetch-depth: 1000 # should be enough to reach the most recent tag
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.github/workflows/publish-pypi.yml

@@ -14,26 +14,26 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.x'
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install wheel twine setuptools
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel twine setuptools
 
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        # The PYPI_PASSWORD must be a pypi token with the "pypi-" prefix with sufficient permissions to upload this package
-        # https://pypi.org/help/#apitoken
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          # The PYPI_PASSWORD must be a pypi token with the "pypi-" prefix with sufficient permissions to upload this package
+          # https://pypi.org/help/#apitoken
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.gitignore

@@ -90,7 +90,7 @@ docs/_build/
 *.tiff
 *.tif
 
-#generated documntation files
+#generated documentation files
 doc/resource/api/generated/
 
 # Enaml
@@ -99,3 +99,6 @@ __enamlcache__/
 
 # PyBuilder
 target/
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.pre-commit-config.yaml

@@ -1,23 +1,96 @@
-exclude: '(v2)/.*'
-default_language_version:
-    python: python3
+ci:
+  autoupdate_commit_msg: "chore(deps): update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  autoupdate_schedule: "quarterly"
+
+exclude: "^({{cookiecutter\\.project_name}}|hooks/pre_gen_project.py$)"
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: "v6.0.0"
     hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
       - id: check-yaml
+      - id: debug-statements
       - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/ambv/black
-    rev: 24.4.2
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.20.0"
     hooks:
-      - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.15.6"
     hooks:
-      - id: isort
-        args: ["--profile", "black"]
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
     hooks:
-      - id: nbstripout
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.19.1"
+    hooks:
+      - id: mypy
+        files: "(src|tests|noxfile.py)"
+        args: []
+        additional_dependencies:
+          - click
+          - markdown-it-py
+          - pytest
+          - nox
+          - orjson
+          - repo-review>=0.10.6
+          - rich
+          - tomli>=2.0.2
+          - types-PyYAML
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.8.1"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/crate-ci/typos
+    rev: "v1.44.0"
+    hooks:
+      - id: typos
+        exclude: ^Gemfile\.lock$
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest|RST|PyLint
+        exclude: (.pre-commit-config.yaml|docs/pages/guides/style\.md)$
+      - id: disallow-words
+        name: Disallow certain words
+        language: pygrep
+        entry: "[Ff]alsey"
+        exclude: .pre-commit-config.yaml$
+      - id: disallow-bad-permalinks
+        name: Disallow _ in permalinks
+        language: pygrep
+        entry: "^permalink:.*_.*"
+      - id: cog
+        name: Cog the pages
+        language: python
+        entry: cog -P -r -I ./helpers
+        files: "^docs/pages/guides/(packaging_compiled|docs|tasks|gha_basic).md|^copier.yml|^docs/_includes/pyproject.md"
+        additional_dependencies: [cogapp, cookiecutter, tomlkit]

README.md

@@ -1,15 +1,22 @@
-pyCHX -- CHX XPCS Data Analysis Packages
-========
+# pyCHX -- CHX XPCS Data Analysis Packages
 
-Repository for data collection and analysis scripts that are useful at the
-CHX beamline at NSLS-II (11-ID) developed by Dr. Yugang Zhang (yuzhang@bnl.gov).
+Repository for data collection and analysis scripts that are useful at the CHX
+beamline at NSLS-II (11-ID) developed by Dr. Yugang Zhang (yuzhang@bnl.gov).
 
 Installation instructions on Linux:
 
-Install miniconda from https://conda.io/miniconda.html. Then create the environment for pyCHX:
+Install miniconda from https://conda.io/miniconda.html. Then create the
+environment for pyCHX:
+
 ```
 conda create --name pyCHX python=3.6 numpy scipy matplotlib
 source activate pyCHX
 pip install -r https://raw.githubusercontent.com/NSLS-II-CHX/pyCHX/master/requirements.txt
 pip install git+https://github.com/NSLS-II-CHX/pyCHX
+
+
+Pixi Install:
+- pixi install: installs only main dependencies
+- pixi install --with dev: installs main and dev dependencies
+- pixi run --with dev pytest: runs pytest with dev tols available
 ```

RELEASE.md

@@ -1,10 +1,9 @@
 Steps for releasing a version of pyCHX
 
-
-* Make sure that you have an up-to-date copy of the master branch.
-* Make an empty commit to serve as a marker in the history. This is technically
-  optional, but it is nice to do. ``git commit --allow-empty -m "REL: v0.0.1"``
-* Now make the tag. This should never be delete, so make sure you are certain.
-  ``git tag v0.0.1``
-* Push the commit up to github: ``git push upstream master``
-* Push the tag also: ``git push upstream v0.0.1``
+- Make sure that you have an up-to-date copy of the master branch.
+- Make an empty commit to serve as a marker in the history. This is technically
+  optional, but it is nice to do. `git commit --allow-empty -m "REL: v0.0.1"`
+- Now make the tag. This should never be delete, so make sure you are certain.
+  `git tag v0.0.1`
+- Push the commit up to github: `git push upstream master`
+- Push the tag also: `git push upstream v0.0.1`