Merge branch 'release/v0.3.0'

.cruft.json

@@ -1,52 +1,44 @@
 {
-    "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
-    "commit": "be1b9cec709f862f8de5132e517a42db90758f04",
-    "checkout": "feature/markdown",
-    "skip": [
-        "src/thermoextrap/__init__.py",
-        "environment.yaml",
-        "HISTORY.md",
-        "AUTHORS.md",
-        "MANIFEST.in",
-        "README.md",
-        "docs/spelling_wordlist.txt",
-        "environment/dev-extras.yaml",
-        "environment/docs-extras.yaml",
-        "environment/test-extras.yaml",
-        "docs/index.md",
-        "docs/installation.md",
-        ".gitignore"
-    ],
-    "context": {
-        "cookiecutter": {
-            "full_name": "William P. Krekelberg",
-            "email": "[email protected]",
-            "github_username": "usnistgov",
-            "pypi_username": "wpk-nist",
-            "conda_channel": "wpk-nist",
-            "project_name": "thermoextrap",
-            "project_slug": "thermoextrap",
-            "_copy_without_render": [
-                "*.html",
-                "docs/_templates/*.rst",
-                "docs/_templates/autosummary/*.rst",
-                "docs/_templates/autodocsumm/*.rst",
-                "docs/_static/*",
-                "docs/_static/css/*",
-                "docs/_static/js/*"
-            ],
-            "project_short_description": "Thermodynamic extrapolation",
-            "version": "0.0.1",
-            "use_pytest": "y",
-            "use_pypi_deployment_with_travis": "n",
-            "command_line_interface": "No command-line interface",
-            "create_author_file": "y",
-            "open_source_license": "NIST license",
-            "sphinx_auto": "autosummary",
-            "sphinx_use_autodocsumm": "y",
-            "sphinx_theme": "sphinx_book_theme",
-            "_template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git"
-        }
-    },
-    "directory": null
+  "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
+  "commit": "cb20a32f67dadb4142be54898a87de1efdce6bd6",
+  "checkout": "feature/markdown",
+  "skip": [
+    "src/thermoextrap/__init__.py",
+    "docs/examples/usage/demo.ipynb",
+    "examples/usage/demo.ipynb",
+    "docs/examples/example-usage.md"
+  ],
+  "context": {
+    "cookiecutter": {
+      "full_name": "William P. Krekelberg",
+      "email": "[email protected]",
+      "github_username": "usnistgov",
+      "pypi_username": "wpk-nist",
+      "conda_channel": "wpk-nist",
+      "project_name": "thermoextrap",
+      "project_slug": "thermoextrap",
+      "_copy_without_render": [
+        "*.html",
+        "docs/_templates/*.rst",
+        "docs/_templates/autosummary/*.rst",
+        "docs/_templates/autodocsumm/*.rst",
+        "docs/_static/css/*",
+        "docs/_static/js/*",
+        "changelog.d/templates/*",
+        "changelog.d/templates/auto-changlog/*"
+      ],
+      "project_short_description": "Thermodynamic extrapolation",
+      "version": "0.0.1",
+      "use_pytest": "y",
+      "use_pypi_deployment_with_travis": "n",
+      "command_line_interface": "No command-line interface",
+      "create_author_file": "y",
+      "open_source_license": "NIST license",
+      "sphinx_auto": "autosummary",
+      "sphinx_use_autodocsumm": "y",
+      "sphinx_theme": "sphinx_book_theme",
+      "_template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git"
+    }
+  },
+  "directory": null
 }

.editorconfig

@@ -0,0 +1,44 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab
+
+[*.mk]
+indent_style = tab
+
+[*.{yaml,yml}]
+indent_size = 2
+
+[*.ini]
+indent_size = 4
+
+[*.json]
+indent_size = 2
+
+
+[*.txt]
+indent_size = 4
+trim_trailing_whitespace = false
+
+
+[*.md]
+indent_size = 2
+max_line_length = 80
+trim_trailing_whitespace = false

.gitignore

@@ -12,7 +12,6 @@ env/
 build/
 develop-eggs/
 dist/
-dist-conda/
 downloads/
 eggs/
 .eggs/
@@ -107,9 +106,7 @@ ENV/
 pyrightconfig.json
 .autoenv.zsh
 .autoenv_leave.zsh
-/docs/generated/
+/docs/**/generated/
 /monkeytype.sqlite3
-/dist-conda/
-/cruft.patch
-/docs/jupyter_execute/
-/docs/reference/generated/
+/dist-conda/*
+!/dist-conda/Makefile

.markdownlint.yaml

@@ -0,0 +1,6 @@
+# Example markdownlint configuration with all properties set to their default value
+
+# Default state for all rules
+default: true
+# disable rules?
+# MD026: false

.pre-commit-config.yaml

@@ -3,86 +3,133 @@
 # pre-commit run --all-files
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+default_install_hook_types:
+  - pre-commit
+  - commit-msg
 repos:
+  #* Top level
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-added-large-files
       - id: check-yaml
-        #     args: [--unsafe]
-  # Ruff
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+  #* Formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.0-alpha.6"
+    hooks:
+      - id: prettier
+        stages: [commit]
+        additional_dependencies:
+          - prettier-plugin-toml
+        exclude: ^tests/lnpy_data/sample_data.json
+  #** markdown
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.6.0
+    hooks:
+      - id: markdownlint-cli2
+        args: ["--style prettier"]
+  #* Linting
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.254'
+    rev: "v0.0.261"
     hooks:
       - id: ruff
-        args: ["--fix"]
-  # isort should run before black as black sometimes tweaks the isort output
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        stages: [manual]
-  # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
-      - id: black-jupyter
+      # - id: black-jupyter
+      # Move to just black.  use nbqa for notebook formatting
+      - id: black
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.13.0"  # replace with latest tag on GitHub
+    rev: "1.13.0"
     hooks:
       - id: blacken-docs
         additional_dependencies:
-          - black==23.1.0
+          - black==23.3.0
         exclude: ^README.md
-  - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
     hooks:
-      - id: blackdoc
-        additional_dependencies: ["black==23.1.0"]
-      - id: blackdoc-autoupdate-black
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+      - id: nbqa-ruff
+        additional_dependencies: [ruff]
+      - id: nbqa-black
+        additional_dependencies: [black]
+
+  #* Commit message
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.0.1
     hooks:
-      - id: codespell
-        types_or: [python, rst, markdown, cython, c]
-        additional_dependencies: [tomli]
-        args: [-I, docs/spelling_wordlist.txt]
+      - id: commitizen
+        stages: [commit-msg]
+
+  #* Manual Linting
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: tox
+        args: ["-e", "lint-mypy"]
+        language: system
+        pass_filenames: false
+        # additional_dependencies: [tox]
+        types: [python]
+        require_serial: true
         stages: [manual]
-  # this should be run before flake8 to
-  # this should be run externally
-  # messes up too many things
-  # - repo: https://github.com/PyCQA/docformatter
-  #   rev: v1.5.0
-  #   hooks:
-  #     - id: docformatter
-  #       args: [--in-place]
+      - id: pyright
+        name: pyright
+        entry: pyright
+        args: []
+        language: system
+        pass_filenames: true
+        # additional_dependencies: [tox]
+        types: [python]
+        require_serial: true
+        stages: [manual]
+  # isort, pyupgrade, flake8 defer to ruff
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        stages: [manual]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+      - id: pyupgrade
+        stages: [manual]
+        args: [--py38-plus]
   - repo: https://github.com/pycqa/flake8
     rev: 6.0.0
     hooks:
       - id: flake8
         stages: [manual]
-        additional_dependencies: [flake8-docstrings]
-        exclude: ^tests/|examples/gpr_active_learning/|src/thermoextrap/legacy/|^docs/conf.py|^setup.py
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
+        additional_dependencies:
+          - flake8-docstrings
+          - Flake8-pyproject
+          # - pep8-naming
+          # - flake8-rst-docstrings
+        exclude: ^tests/|^src/thermoextrap/tests/|^docs/conf.py|^setup.py|example/gpr_active_learning/|src/thermoextrap/legacy
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
     hooks:
-      - id: mypy
-        # `properies` & `asv_bench` are copied from setup.cfg.
-        # `_typed_ops.py` is added since otherwise mypy will complain (but notably only in pre-commit)
-        exclude: properties|asv_bench|_typed_ops.py|conf.py
-        # This is slow and so we take it out of the fast-path; requires passing
-        # `--hook-stage manual` to pre-commit
+      - id: nbqa-pyupgrade
+        additional_dependencies: [pyupgrade]
         stages: [manual]
-        additional_dependencies: [types-pkg_resources, typing-extensions==3.10.0.0, numpy]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+        args: [--py38-plus]
+      - id: nbqa-isort
+        additional_dependencies: [isort]
+        stages: [manual]
+  #** spelling
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
     hooks:
-      - id: pyupgrade
+      - id: codespell
+        types_or: [python, rst, markdown, cython, c]
+        additional_dependencies: [tomli]
+        args: [-I, docs/spelling_wordlist.txt]
         stages: [manual]
-        args:
-          - --py38-plus
-          # remove on f-strings in Py3.7
-          - --keep-percent-format

.prettierrc.yaml

@@ -0,0 +1 @@
+proseWrap: "always"