Merge branch 'release/v0.5.0'

.cruft.json

@@ -1,7 +1,7 @@
 {
-  "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
-  "commit": "49d100c749e6cfa2cba3460ed06e4a06be07cc63",
-  "checkout": "feature/nox",
+  "template": "https://github.com/usnistgov/cookiecutter-nist-python.git",
+  "commit": "61580376ae0c11b954b1d78c9812f5979bc81622",
+  "checkout": "develop",
   "skip": [
     "src/thermoextrap/__init__.py",
     "docs/examples/usage/demo.ipynb",
@@ -10,34 +10,21 @@
   ],
   "context": {
     "cookiecutter": {
+      "project_name": "thermoextrap",
+      "project_slug": "thermoextrap",
+      "project_short_description": "Thermodynamic extrapolation",
       "full_name": "William P. Krekelberg",
       "email": "[email protected]",
       "github_username": "usnistgov",
       "pypi_username": "wpk-nist",
       "conda_channel": "conda-forge",
-      "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/*.j2",
-        "changelog.d/templates/auto-changelog/*.jinja2"
-      ],
-      "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",
+      "command_line_interface": "none",
+      "sphinx_use_autodocsumm": true,
       "sphinx_theme": "sphinx_book_theme",
-      "_template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git"
+      "year": "2020",
+      "__answers": "",
+      "_copy_without_render": [],
+      "_template": "https://github.com/usnistgov/cookiecutter-nist-python.git"
     }
   },
   "directory": null

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.gitignore

@@ -39,6 +39,7 @@ pip-delete-this-directory.txt
 htmlcov/
 .tox/
 .nox/
+envs/
 .coverage
 .coverage.*
 .cache
@@ -99,18 +100,35 @@ ENV/
 # mkdocs documentation
 /site
 
+# NOTE: use `/.mypy_cache/`, etc because want to flag those in other
 # mypy
 .mypy_cache/
 
+# pytpe
+.pytype/
+
+# ruff
+.ruff_cache
+
+# PDF output
+README.pdf
+
 # IDE settings
 .vscode/
 pyrightconfig.json
 .autoenv.zsh
 .autoenv_leave.zsh
-.noxconfig.toml
+config/userconfig.toml
 cruft.patch
 /docs/**/generated/
 /monkeytype.sqlite3
 /dist-conda/
 /tmp/
 /thermoextrap-feedstock*/
+/src/**/_version.py
+tuna-loadtime.log
+/requirements/py*-dev-user.yaml
+/requirements/dev-user.txt
+/requirements/lock/py*-dev-user-conda-lock.yml*
+/requirements/lock/py*-dev-user.txt*
+/README.pdf

.pre-commit-config.yaml

@@ -1,4 +1,3 @@
----
 # pre-commit install
 # pre-commit run --all-files
 # See https://pre-commit.com for more information
@@ -7,129 +6,154 @@ default_install_hook_types:
   - pre-commit
   - commit-msg
 repos:
-  #* Top level
+  # * Top level
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
       - id: check-added-large-files
-      - id: check-yaml
-      - id: check-json
+      - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-symlinks
+      - id: check-yaml
+      - id: check-json
       - id: check-toml
-  #* Formatting
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+  # * Sync dependencies
+  - repo: https://github.com/mxr/sync-pre-commit-deps
+    rev: v0.0.1
+    hooks:
+      - id: sync-pre-commit-deps
+
+  # * Pyproject-fmt
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: 1.7.0
+    hooks:
+      - id: pyproject-fmt
+        args: [--indent=4, --keep-full-version]
+        files: ^pyproject.toml$
+
+  # * Prettier
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.0-alpha.6"
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+        alias: markdownlint
         stages: [commit]
         additional_dependencies:
           - prettier-plugin-toml
-        exclude: ^tests/lnpy_data/sample_data.json
-  #** markdown
+
+  # * Markdown
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.6.0
+    rev: v0.12.1
     hooks:
       - id: markdownlint-cli2
-        args: ["--style prettier"]
-  #* Linting
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    # Ruff version.
-    rev: "v0.0.261"
-    hooks:
-      - id: ruff
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      # - id: black-jupyter
-      # Move to just black.  use nbqa for notebook formatting
-      - id: black
+        alias: markdownlint
+        args: [--style, prettier]
+
+  # * Linting
+  # To be replace by ruff analog when I find one ...
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.13.0"
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
         additional_dependencies:
-          - black==23.3.0
-        # exclude: ^README.md
+          - black==24.2.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.2
+    hooks:
+      - id: ruff
+        types_or: &ruff-types-or [python, pyi, jupyter]
+        args: [--fix, --show-fixes]
+      - id: ruff-format
+        types_or: *ruff-types-or
+
+  # * Spelling
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies: [tomli]
+        args: [-I, docs/spelling_wordlist.txt]
+        exclude_types: [jupyter]
+
+  # * Notebook spelling
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.4
+    hooks:
+      - id: nbqa
+        alias: nbqa-codespell
+        name: nbqa-codespell
+        additional_dependencies: &codespell-deps [codespell==2.2.6, tomli] # make sure same as above
+        args:
+          [codespell, --ignore-words=docs/spelling_wordlist.txt, --nbqa-shell]
+      - id: nbqa
+        alias: nbqa-codespell
+        name: nbqa-codespell-markdown
+        additional_dependencies: *codespell-deps
+        args:
+          [
+            codespell,
+            --ignore-words=docs/spelling_wordlist.txt,
+            --nbqa-shell,
+            --nbqa-md,
+          ]
+
+  # * Strip out metadata from notebooks
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
     hooks:
-      - id: nbqa-ruff
-        additional_dependencies: [ruff]
-      - id: nbqa-black
-        additional_dependencies: [black]
+      - id: nbstripout
+        args: [
+            --keep-output, # keep output (needed for nbval testing)
+            --keep-count, # Errors with nbval without this...
+            --extra-keys, # strip out kernelspec.  If use this, always have to reselect kernel when open a notebook...
+            "metadata.kernelspec metadata.kernel_spec",
+          ]
 
-  #* Commit message
+  # * Commit message
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v3.0.1
+    rev: v3.18.3
     hooks:
       - 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]
-      - 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]
+  # * Manual Linting ------------------------------------------------------------
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.15.1
     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
-          - 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
+    rev: 1.8.4
     hooks:
       - id: nbqa-pyupgrade
         additional_dependencies: [pyupgrade]
         stages: [manual]
         args: [--py38-plus]
-      - id: nbqa-isort
-        additional_dependencies: [isort]
+
+  # ** typos
+  # Probably stick with codespell, but this might also be nice...
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.19.0
+    hooks:
+      - id: typos
         stages: [manual]
-  #** spelling
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+        exclude: "[.]ipynb$"
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.4
     hooks:
-      - id: codespell
-        types_or: [python, rst, markdown, cython, c]
-        additional_dependencies: [tomli]
-        args: [-I, docs/spelling_wordlist.txt]
+      - id: nbqa
+        alias: nbqa-typos
+        name: nbqa-typos
+        additional_dependencies: &typos-deps [typos==1.19.0] # make sure save version as above.
+        stages: [manual]
+        args: [typos, --nbqa-shell]
+      - id: nbqa
+        alias: nbqa-typos
+        name: nbqa-typos-markdown
+        additional_dependencies: *typos-deps
         stages: [manual]
+        args: [typos, --nbqa-shell, --nbqa-md]

.prettierignore

@@ -0,0 +1,11 @@
+# Ignore file for prettier
+# Similar to .gitignore
+
+# Use pyproject-fmt for pyproject.toml
+pyproject.toml
+
+# Don't fix yaml files under requirements/lock.  These are created by conda-lock.
+/requirements/lock/*.y*ml
+
+# Don't fix copier answers
+.copier-answers.y*ml

AUTHORS.md

@@ -2,8 +2,8 @@
 
 ## Development Leads
 
-- Jacob Monroe \<[email protected]>
-- William P. Krekelberg \<[email protected]>
+- Jacob Monroe <[email protected]>
+- William P. Krekelberg <[email protected]>
 
 ## Contributors