Move to pyproject.toml, reorganize documentation, and refactor interpolation function on Strand (#193)

* move away from setup.cfg/setup.py

* more fixes to pyproject

* some refactoring of interp functions, move read time function

* reorganize docs, use pydata theme

* fix tox file

* fix datetime deprecation

* don't lint bat files

* make precommit happy

* add fixture back

* fix docstring

Author: wtbarnes

.coveragerc

@@ -18,7 +18,6 @@ jobs:
       envs: |
         - macos: py312
         - windows: py312
-        - linux: py310
         - linux: py311
         - linux: py312
         - linux: py313

.github/workflows/test.yml

@@ -67,4 +67,4 @@ target/
 .pytest_cache
 
 # Project specific
-pydrad/_version.py
+pydrad/version.py

.gitignore

@@ -1,71 +1,43 @@
+ci:
+  autofix_prs: false
+  autoupdate_schedule: quarterly
+
 repos:
-  # The warnings/errors we check for here are:
-  # E101 - mix of tabs and spaces
-  # W191 - use of tabs
-  # W291 - trailing whitespace
-  # W292 - no newline at end of file
-  # W293 - trailing whitespace
-  # W391 - blank line at end of file
-  # E111 - 4 spaces per indentation level
-  # E112 - 4 spaces per indentation level
-  # E113 - 4 spaces per indentation level
-  # E303 - too many blank lines (3)
-  # E304 - blank lines found after function decorator
-  # E305 - expected 2 blank lines after class or function definition
-  # E306 - expected 1 blank line before a nested definition
-  # E502 - the backslash is redundant between brackets
-  # E722 - do not use bare except
-  # E901 - SyntaxError or IndentationError
-  # E902 - IOError
-  # F822: undefined name in __all__
-  # F823: local variable name referenced before assignment
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.12.7"
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-use-pathlib]
-        args: ['--count', '--select', 'E101,W191,W291,W292,W293,W391,E111,E112,E113,E303,E304,E306,E502,E722,E901,E902,F822,F823,PL100,PL102,PL103,PL104,PL105,PL110,PL112,PL113,PL18,PL120,PL122,PL123']
+      - id: ruff
+        args: ["--fix"]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 6.0.1
+    hooks:
+    - id: isort
+      name: isort
+      entry: isort
+      require_serial: true
+      language: python
+      types:
+      - python
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt|.pro)$|pydrad/configure/(templates|data)/.*"
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json|.dat|.cfg|.h|.bat)$"
       - id: check-yaml
       - id: debug-statements
       - id: check-added-large-files
       - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.bib|tca.*)$|pydrad/configure/(templates|data)/.*"
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json|.bib|tca.*|.dat|.cfg|.h|.bat)$"
       - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|.bib|tca.*)$|pydrad/configure/(templates|data)/.*"
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-    - id: pyupgrade
-      args: [--keep-runtime-typing, --py38-plus]
-      files: ^fiasco/
+        exclude: ".*(.fits|.fts|.fit|.txt|.bib|.pro|.asdf|.json|tca.*|.dat|.cfg|.h|.bat)$"
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.4.1
     hooks:
       - id: codespell
-        args: ['--config setup.cfg']
-
-  - repo: https://github.com/MarcoGorelli/absolufy-imports
-    rev: v0.3.1
-    hooks:
-    - id: absolufy-imports
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-    - id: isort
-      name: isort
-      entry: isort
-      require_serial: true
-      language: python
-      types:
-      - python
+        additional_dependencies:
+        - tomli

.pre-commit-config.yaml

@@ -1,25 +1,30 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.11"
+    python: "mambaforge-latest"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow || true
+    pre_install:
+      - git update-index --assume-unchanged .rtd-environment.yml docs/conf.py
+
+conda:
+  environment: .rtd-environment.yml
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
+  builder: html
   configuration: docs/conf.py
+  fail_on_warning: false
+
+formats:
+  - htmlzip
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-      - docs
-      - all
+    - method: pip
+      extra_requirements:
+        - all
+        - docs
+      path: .

.readthedocs.yml

@@ -0,0 +1,7 @@
+name: rtd_fiasco
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - pip
+  - graphviz!=2.42.*,!=2.43.*

.rtd-environment.yml

@@ -5,6 +5,7 @@
 import pytest
 
 import pydrad.configure
+
 from pydrad.configure.util import get_clean_hydrad
 
 
@@ -112,7 +113,7 @@ def get_configuration_dict():
     }
 
 
-@pytest.fixture(scope='function')
+@pytest.fixture
 def configuration():
     return pydrad.configure.Configure(get_configuration_dict(), freeze_date=True)
 

conftest.py

@@ -14,7 +14,17 @@ help:
 
 .PHONY: help Makefile
 
+html-noplot:
+	@$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf $(BUILDDIR)
+	rm -rf ./generated
+	rm -rf ./api

docs/Makefile

@@ -1,3 +1,5 @@
+.. _pydrad-citation:
+
 Citing pydrad
 ===============
 

docs/citation.rst

@@ -4,3 +4,10 @@ pydrad configure
 .. automodapi:: pydrad.configure
     :no-heading:
     :no-inheritance-diagram:
+
+.. automodapi:: pydrad.configure.util
+    :no-heading:
+    :no-inheritance-diagram:
+    :no-main-docstr:
+    :skip: MissingParameter
+    :skip: HYDRADError