Merge branch 'main' into test-refactoring

.github/workflows/testing.yml

@@ -26,24 +26,24 @@ jobs:
 
         - name: Tests, Python 3.12, Windows
           os: windows-latest
-          noxenv: tests-3.12
+          noxenv: tests
           python: '3.12'
           noxposargs: --durations=10
 
         - name: Tests, Python 3.11, Windows
           os: windows-latest
-          noxenv: tests-3.11
+          noxenv: tests
           python: '3.11'
           noxposargs: --durations=10
 
         - name: Tests, Python 3.10, macOS
           os: macos-latest
-          noxenv: tests-3.10
+          noxenv: tests
           python: '3.10'
 
         - name: Tests, Python 3.10, Linux
           os: ubuntu-latest
-          noxenv: tests-3.10
+          noxenv: tests
           python: '3.10'
 
         - name: Import XRTpy, Python 3.10, Linux
@@ -109,4 +109,4 @@ jobs:
         pandoc --version
 
     - name: Build documentation
-      run: nox -s build_docs_nitpicky -- -q
+      run: nox -s docs

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ ci:
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-ast
     name: validate Python code
@@ -23,7 +23,7 @@ repos:
   - id: check-yaml
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.29.2
+  rev: 0.29.3
   hooks:
   - id: check-github-workflows
 
@@ -47,11 +47,6 @@ repos:
     args: [--autofix]
   - id: pretty-format-yaml
     args: [--autofix]
-    # For the labeler GitHub Action, labels with spaces in them must
-    # be put in quotes. However, the pretty-format-yaml hook will
-    # remove the quotes which will break that action (and certain other
-    # actions).
-    exclude: .github/labeler.yml|.pre-commit-search-and-replace.yaml
 
 - repo: https://github.com/MarcoGorelli/absolufy-imports
   rev: v0.3.1
@@ -62,8 +57,6 @@ repos:
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
-  - id: python-check-blanket-noqa
-    name: noqa comments have an error code
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
   - id: text-unicode-replacement-char
@@ -79,10 +72,10 @@ repos:
     exclude: .*\.fits
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.3
+  rev: v0.6.9
   hooks:
   - id: ruff
-    name: ruff (see https://docs.astral.sh/ruff/rules)
+    name: ruff
     args: [--fix]
   - id: ruff-format
     name: autoformat source code with ruff formatter
@@ -93,16 +86,13 @@ repos:
   - id: blacken-docs
     name: autoformat code blocks in docs
     additional_dependencies:
-    - black==24.1.1
+    - black
 
 - repo: https://github.com/nbQA-dev/nbQA
   rev: 1.8.7
   hooks:
   - id: nbqa-check-ast
     name: validate Python notebooks
-  - id: nbqa-ruff
-    name: ruff for notebooks (see https://docs.astral.sh/ruff/rules)
-    args: [--fix, '--select=A,ARG,B,BLE,C,C4,E,F,FLY,I,INT,ISC,PERF,PIE,PLC,PLE,PYI,Q003,RET,RSE,SIM,TID,TRY,UP,W', '--ignore=B018,E402,E501,PLC2401,TRY003']
   - id: nbqa-black
     additional_dependencies:
-    - black==24.1.1
+    - black

.readthedocs.yaml

@@ -7,9 +7,9 @@ formats:
 - htmlzip
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: '3.11'
+    python: latest
   apt_packages:
   - graphviz
   jobs:

.ruff.toml

@@ -0,0 +1,76 @@
+target-version = "py310"
+show-fixes = true
+extend-exclude = [
+  ".jupyter",
+  "__pycache__",
+  "_build",
+  "_dev",
+]
+
+[lint]
+# Find info about ruff rules at: https://docs.astral.sh/ruff/rules
+extend-select = [
+  "ARG", # flake8-unused-arguments
+  "B", # flake8-bugbear
+  "BLE", # flake8-blind-except
+  "C4", # flake8-comprehensions
+  "C90", # mccabe
+  "COM818", # trailing-comma-on-bare-tuple
+  "FBT003", # flake8-boolean-trap
+  "FLY", # flynt
+  "I", # isort
+  "ICN", # flake8-import-conventions
+  "INP", # flake8-no-pep420
+  "INT", # flake8-gettext
+  "ISC", # flake8-implicit-str-concat
+  "N", # pep8-naming
+  "NPY", # numpy-deprecated-type-alias
+  "PD", # pandas-vet
+  "PERF", # perflint
+  "PGH", # pygrep-hooks
+  "PIE", # flake8-pie
+  "PLC", # pylint convention
+  "PLE", # pylint errors
+  "PLW", # pylint warnings
+  "PT", # flake8-pytest-style
+  "PTH", # flake8-use-pathlib
+  "PYI", # flake8-pyi
+  "RSE", # flake8-raise
+  "RUF005",# collection-literal-concatenation
+  "RUF006", # asyncio-dangling-task
+  "RUF007", # pairwise-over-zipped
+  "RUF008", # mutable-dataclass-default
+  "RUF009", # function-call-in-dataclass-default-argument
+  "RUF010", # explicit-f-string-type-conversion
+  "RUF013", # implicit-optional
+  "RUF015", # unnecessary-iterable-allocation-for-first-element
+  "RUF016", # invalid-index-type
+  "RUF100", # unused-noqa
+  "RUF200", # invalid-pyproject-toml
+  "S", # flake8-bandit
+  "SIM", # flake8-simplify
+  "TCH", # flake8-type-checking
+  "TID", # flake8-tidy-imports
+  "TRY", # tryceratops
+  "UP", # pyupgrade
+  "W", # pycodestyle warnings
+]
+ignore = [
+  "C901", # is too complex
+  "E501", # line-too-long
+  "ISC001", # single-line-implicit-string-concatenation (formatter conflict)
+  "N802", # invalid-function-name
+  "N803", # invalid-argument-name
+  "N806", # non-lowercase-variable-in-function
+  "N816", # mixed-case-variable-in-global-scope
+  "PLC2401", # non-ascii-name
+  "S101", # asserts
+  "SIM108", # if-else-block-instead-of-if-exp
+  "TRY003", # raise-vanilla-args
+]
+
+[lint.per-file-ignores]
+"docs/conf.py" = [
+  "E402",  # Module imports not at top of file
+  "INP001",  # Implicit-namespace-package. The examples are not a package.
+]

README.md

@@ -5,10 +5,8 @@
 [![Read the Docs Status](https://readthedocs.org/projects/xrtpy/badge/?version=latest&logo=twitter)](http://xrtpy.readthedocs.io/en/latest/?badge=latest)
 [![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat&logo=astropy)](http://www.astropy.org/)
 
-XRTpy is a Python package being developed for the analysis of observations
-made by the X-Ray Telescope (XRT) on the *Hinode* spacecraft.
+XRTpy is a Python package being developed for the analysis of observations made by the X-Ray Telescope (XRT) on the **Hinode** spacecraft.
 
 ## Acknowledgements
 
-The development of XRTpy is supported by NASA contract NNM07AB07C to the
-Smithsonian Astrophysical Observatory.
+The development of XRTpy is supported by NASA contract **NNM07AB07C** to the Smithsonian Astrophysical Observatory.

docs/changelog/index.rst

@@ -11,7 +11,6 @@ including bug fixes and changes to the application programming interface
 .. toctree::
    :maxdepth: 1
 
-   dev
    0.4.0
    0.3.0
    0.2.0

docs/conf.py

@@ -35,11 +35,9 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.todo",
     "nbsphinx",
-    "sphinx_changelog",
     "sphinx_copybutton",
     "sphinx_gallery.load_style",
     "IPython.sphinxext.ipython_console_highlighting",
-    "sphinx_changelog",
     "sphinx_issues",
     "sphinxcontrib.bibtex",
     "hoverxref.extension",

docs/contributing/acknowledging_xrtpy.rst

@@ -0,0 +1,30 @@
+.. _citation_guide:
+
+===============================================
+Citing XRTpy in Publications and Presentations
+===============================================
+
+
+If XRTpy has been useful in your research, we encourage you to consider including a citation or acknowledgment in your work. Below are suggested formats to credit XRTpy in your scientific papers, posters, or presentations. While this is not required, it is greatly appreciated.
+
+Suggested Citations
+===================
+
+For a scientific paper
+----------------------
+You may use the following format to cite XRTpy in your publications:
+
+    "We acknowledge the use of XRTpy (v0.4.1) for Hinode X-Ray Telescope data analysis, available at https://xrtpy.readthedocs.io/ (Velasquez et al. 2024, JOSS, DOI: 10.21105/joss.06396)."
+
+For a poster or presentation
+----------------------------
+If you are presenting work that involves XRTpy in a poster or presentation, you may use the following acknowledgment:
+
+    "This work made use of XRTpy (v0.4.1), a Python package for solar
+    Hinode X-Ray Telescope data analysis, available at https://xrtpy.readthedocs.io/ (Velasquez et al. 2024, JOSS, DOI: 10.21105/joss.06396)."
+
+References
+==========
+Velasquez, J., Murphy, N., Reeves, K. K., Slavin, J., Weber, M., & Barnes, W. (2024). XRTpy: A Hinode-X-Ray Telescope Python Package. The Journal of Open Source Software, 9(100), 6396. https://doi.org/10.21105/joss.06396
+
+.. _joss_citation: https://doi.org/10.21105/joss.06396

docs/contributing/index.rst

@@ -10,3 +10,4 @@ Contributor Guide
    contributing
    installation_for_development
    release_guide
+   acknowledging_xrtpy

docs/index.rst

@@ -3,7 +3,7 @@
 .. _xrtpy-documentation:
 
 .. image:: images/XRTpy_logo.png
-   :alt: PlasmaPy logo
+   :alt: XRTpy logo
    :align: right
    :scale: 40%
 

docs/notebooks/getting_started/A_Practical_Guide_to_Data_Extraction_and_Visualization.ipynb

@@ -79,8 +79,8 @@
    "outputs": [],
    "source": [
     "# Standard library imports for file and temporary directory management\n",
-    "import os\n",
     "import tempfile\n",
+    "from pathlib import Path\n",
     "\n",
     "# Counting occurrences of unique elements\n",
     "# creating and managing images and videos\n",
@@ -1066,7 +1066,7 @@
     "        plt.tight_layout()\n",
     "\n",
     "        # Saving the frame\n",
-    "        frame_path = os.path.join(frames_dir, f\"frame_{i:04d}.png\")\n",
+    "        frame_path = Path(frames_dir) / f\"frame_{i:04d}.png\"\n",
     "        plt.savefig(frame_path)\n",
     "        plt.close(fig)\n",
     "        frames.append(frame_path)\n",
@@ -1084,8 +1084,8 @@
     "\n",
     "    # Cleanup: Remove temporary frames and directory\n",
     "    for frame_path in frames:\n",
-    "        os.remove(frame_path)\n",
-    "    os.rmdir(frames_dir)\n",
+    "        Path(frame_path).unlink()\n",
+    "    Path(frames_dir).rmdir()\n",
     "\n",
     "    if processing:\n",
     "        print(\n",