Maintenance update project and dependencies (#428)

* Update project use project.toml and move config into own files

* Fix most of the tests

* ruff-check, ruff-format and codespell

* Some spelling mistakes left need to check the meaning

* More updates and fixes

* Few more small fixes

* Fix doc build

* Revert unintentional spelling correction in IDB sql script.

* Update tox test dep name

* Add version.py to git

* Skip unclear test add skipped test for later

* Update workflow python version

* Add remote data to github CI

Author: samaloney

.codespellrc

@@ -0,0 +1,21 @@
+[codespell]
+skip = ,*.fits,*.fts,*.header,*.json,*.xsh,*cache*,*egg*,*extern*,.git,.idea,.tox,_build,*truncated,*.svg,.asv_env,.history,*.sql
+ignore-words-list =
+    alog,
+    nd,
+    nin,
+    observ,
+    ot,
+    te,
+    upto,
+    afile,
+    precessed,
+    process,
+    livetime,
+    technik,
+    thirdparty,
+    commutated,
+    anc,
+    soop,
+    CODIN,
+    allright

.coveragerc

@@ -0,0 +1,32 @@
+[run]
+omit =
+  stixcore/_sunpy_init*
+  stixcore/conftest.py
+  stixcore/*setup_package*
+  stixcore/tests/*
+  stixcore/*/tests/*
+  stixcore/extern/*
+  stixcore/version*
+  */stixcore/_sunpy_init*
+  */stixcore/conftest.py
+  */stixcore/*setup_package*
+  */stixcore/tests/*
+  */stixcore/*/tests/*
+  */stixcore/extern/*
+  */stixcore/version*
+
+[report]
+exclude_lines =
+  # Have to re-enable the standard pragma
+  pragma: no cover
+  # Don't complain about packages we have installed
+  except ImportError
+  # Don't complain if tests don't hit assertions
+  raise AssertionError
+  raise NotImplementedError
+  # Don't complain about script hooks
+  def main\(.*\):
+  # Ignore branches that don't pertain to this version of Python
+  pragma: py{ignore_python_version}
+  # Don't complain about IPython completion helper
+  def _ipython_key_completions_

.github/workflows/end2end_run.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
 
     steps:
     - name: Checkout github repo (+ download lfs dependencies)
@@ -41,4 +41,4 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: end2end test with pytest
       run: |
-        pytest -p no:warnings --doctest-rst -m "end2end" --pyargs stixcore
+        pytest -p no:warnings --doctest-rst -m "end2end" --pyargs stixcore --remote-data=any

.gitignore

@@ -153,7 +153,6 @@ docs/_build
 docs/generated
 docs/api
 docs/whatsnew/latest_changelog.txt
-stixcore/version.py
 htmlcov/
 *.prof
 pdpp.html
@@ -165,3 +164,4 @@ stixcore/data/test/products/end2end/
 monitor_status.json
 stixcore/data/test/idb/v2.26.38/idb.sqlite
 .python-version
+sunpy/_version.py

.isort.cfg

@@ -0,0 +1,14 @@
+[settings]
+balanced_wrapping = True
+skip=docs/conf.py
+default_section = THIRDPARTY
+include_trailing_comma = True
+known_astropy = astropy, asdf
+known_first_party = stixcore
+length_sort = False
+length_sort_sections=stdlib
+line_length = 100
+multi_line_output = 3
+no_lines_before = LOCALFOLDER
+sections = STDLIB, THIRDPARTY, ASTROPY, FIRSTPARTY, LOCALFOLDER
+honor_noqa = True

.pre-commit-config.yaml

@@ -1,53 +1,38 @@
+exclude: ".*(.csv|.fits|.fts|.fit|.header|.txt|tca.*|.json|.asdf)$|^CITATION.rst|(^|/)data/test(/|$)"
 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: 3.7.9
+    # This should be before any formatting hooks like isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.12.2"
     hooks:
-      - id: flake8
-        args: ['--count', '--select', 'C90,E,W,F']
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|__init__.py|docs/conf.py)$"
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
-    hooks:
-      - id: autoflake
-        args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|__init__.py|docs/conf.py)$"
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
+      - id: ruff-check
+        args: ["--fix"]
+      # Run the formatter.
+      - id: ruff-format
+  - repo: https://github.com/PyCQA/isort
+    rev: 6.0.1
     hooks:
       - id: isort
-        args: ['--sp','setup.cfg']
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|cm/__init__.py|sunpy/extern|docs/conf.py)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt)$"
       - id: check-yaml
       - id: debug-statements
       - id: check-added-large-files
+        args: ["--enforce-all", "--maxkb=1054"]
+        exclude: ""
       - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
       - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        args: ["--write-changes"]
+
+ci:
+  autofix_prs: false
+  autoupdate_schedule: "quarterly"

.readthedocs.yml

@@ -19,7 +19,7 @@ formats: []
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

.zenodo.json

@@ -13,7 +13,7 @@
             "name": "Nicky Hochmuth",
             "orcid": "0009-0005-3785-7643",
             "affiliation": "Ateleris GmbH Switzerland"
-        },
+        }
     ],
     "access_right": "open"
 }

MANIFEST.in

@@ -1,19 +1,21 @@
-include README.rst
-include CHANGES.rst
-include setup.cfg
-include LICENSE.rst
-include pyproject.toml
+# Exclude specific files
+# All files which are tracked by git and not explicitly excluded here are included by setuptools_scm
+exclude .codecov.yaml
+exclude .editorconfig
+exclude .gitattributes
+exclude .gitignore
+exclude .mailmap
+exclude .pre-commit-config.yaml
+exclude .readthedocs.yaml
+exclude .rtd-environment.yml
+exclude .zenodo.json
+exclude tox.ini
 
-recursive-include stixcore *.pyx *.c *.pxd
-recursive-include docs *
-recursive-include licenses *
-recursive-include cextern *
-recursive-include scripts *
-recursive-include stixcore/config/data *
-recursive-include stixcore/data *
-
-prune build
-prune docs/_build
-prune docs/api
+# Prune folders
+prune .circleci
+prune .github
+prune changelog
+prune sunpy/_dev
 
-global-exclude *.pyc *.o
+# Add back in submodule data
+recursive-include stixcore/config/data *

azure-pipelines.yml

@@ -3,7 +3,7 @@ variables:
   CI_NAME: Azure Pipelines
   CI_BUILD_ID: $(Build.BuildId)
   CI_BUILD_URL: "https://dev.azure.com/https://github.com/i4Ds/STIXCore.git/_build/results?buildId=$(Build.BuildId)"
-  CIBW_BUILD: cp39-* cp310-* cp311-*
+  CIBW_BUILD: cp311-* cp312-* cp313-*
   CIBW_SKIP: "*-win32 *-manylinux1_i686"
 
 resources:
@@ -35,17 +35,17 @@ jobs:
     toxdeps: tox-pypi-filter
     submodules: true
     coverage: codecov
-    default_python: '3.9'
+    default_python: '3.11'
     envs:
-      - macos: py39
-        name: py39_mac
+      - macos: py311
+        name: py311_mac
         coverage: false
 
-      - windows: py39
-        name: py39_win
+      - windows: py311
+        name: py311_win
 
-      - linux: py39
-        name: py39_linux
+      - linux: py311
+        name: py311_linux
 
       - linux: codestyle
         name: codestyle
@@ -67,6 +67,6 @@ jobs:
         # - wheels_macos
         - sdist
       dependsOn:
-        - py39_test
-        - py310_test
-        - py311_test
+        - py311_mac
+        - py311_win
+        - py311_linux