Bump minimum python and dependancies (#234)

* Update cruft with batchpr

* bump

* Spec 0 bumps

* rtd python bump

* ruff

* more updates

* Update RTD env for sqlite error

* Update numdifftools version and filtered warnings

* Add breaking changelog.

* Update .github/workflows/sub_package_update.yml

Copilot typo fix

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Shane Maloney <[email protected]>
Co-authored-by: Shane Maloney <[email protected]>
Co-authored-by: Copilot <[email protected]>

Author: 3 people

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "2d254ec79b0b2d9dfb8d7d08ebd83fa6da234b46",
+  "commit": "164646d882aa2e972d305c54778aaaf35f707464",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -17,7 +17,7 @@
       "changelog_url": "",
       "issue_tracker_url": "",
       "license": "BSD 3-Clause",
-      "minimum_python_version": "3.10",
+      "minimum_python_version": "3.12",
       "use_compiled_extensions": "n",
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
@@ -32,7 +32,7 @@
         ".github/workflows/sub_package_update.yml"
       ],
       "_template": "https://github.com/sunpy/package-template",
-      "_commit": "2d254ec79b0b2d9dfb8d7d08ebd83fa6da234b46"
+      "_commit": "164646d882aa2e972d305c54778aaaf35f707464"
     }
   },
   "directory": null

.github/workflows/ci.yml

@@ -42,10 +42,10 @@ jobs:
   sdist_verify:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - run: python -m pip install -U --user build
       - run: python -m build . --sdist
       - run: python -m pip install -U --user twine
@@ -60,18 +60,19 @@ jobs:
       toxdeps: tox-pypi-filter
       posargs:
       envs: |
-        - windows: py311
+        - linux: py314
+        - windows: py312
         - macos: py312
-        - linux: py310-oldestdeps
-        - linux: py313-devdeps
+        - linux: py312-oldestdeps
+        - linux: py314-devdeps
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   docs:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v2
     with:
-      default_python: '3.12'
+      default_python: '3.13'
       submodules: false
       pytest: false
       toxdeps: tox-pypi-filter
@@ -94,7 +95,7 @@ jobs:
     needs: [test, docs]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v2
     with:
-      python-version: '3.12'
+      python-version: '3.13'
       test_extras: 'tests'
       test_command: 'pytest -p no:warnings --doctest-rst --pyargs sunkit_spex'
       submodules: false

.github/workflows/sub_package_update.yml

@@ -1,9 +1,6 @@
 # This template is taken from the cruft example code, for further information please see:
 # https://cruft.github.io/cruft/#automating-updates-with-github-actions
 name: Automatic Update from package template
-permissions:
-    contents: write
-    pull-requests: write
 
 on:
   # Allow manual runs through the web UI
@@ -19,14 +16,17 @@ on:
 jobs:
   update:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     strategy:
       fail-fast: true
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.11"
+          python-version: "3.14"
 
       - name: Install Cruft
         run: python -m pip install git+https://github.com/Cadair/cruft@patch-p1
@@ -93,3 +93,70 @@ jobs:
             If this pull request has been opened as a draft there are conflicts which need fixing.
 
             **To run the CI on this pull request you will need to close it and reopen it.**
+
+  report-fail:
+    if: failure()
+    needs: [update]
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Open an issue if workflow fails
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ github.token }}
+          # This script is adapted from https://github.com/scientific-python/issue-from-pytest-log-action
+          # Under MIT license (c) Scientific Python Developers
+          script: |
+            const fs = require('fs');
+
+            // Edit these if needed for your repo
+            const variables = {
+              owner: context.repo.owner,
+              name: context.repo.repo,
+              label: "Infrastructure",
+              creator: "app/github-actions",
+              title: "SunPy Package Template auto-update failed."
+            };
+
+            const logs = 'The package update workflow failed.'
+            const workflow_url = `https://github.com/${process.env.GITHUB_REPOSITORY}/actions/runs/${process.env.GITHUB_RUN_ID}`;
+            const issue_body = `[Workflow Run URL](${workflow_url})\n${logs}`;
+
+            const query_string = `repo:${variables.owner}/${variables.name} author:${variables.creator} label:${variables.label} is:open in:title ${variables.title}`;
+
+            // Run GraphQL query against GitHub API to find the most recent open issue used for reporting failures
+            const query = `query {
+              search(query: "${query_string}", type:ISSUE, first: 1) {
+                edges {
+                  node {
+                    ... on Issue {
+                      body
+                      id
+                      number
+                    }
+                  }
+                }
+              }
+            }`;
+
+            const result = await github.graphql(query);
+
+            // If no issue is open, create a new issue,
+            // else update the body of the existing issue.
+            if (result.search.edges.length === 0) {
+              github.rest.issues.create({
+                owner: variables.owner,
+                repo: variables.name,
+                body: issue_body,
+                title: variables.title,
+                labels: [variables.label],
+              });
+            } else {
+              github.rest.issues.update({
+                owner: variables.owner,
+                repo: variables.name,
+                issue_number: result.search.edges[0].node.number,
+                body: issue_body
+              });
+            }

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.7"
+    rev: "v0.14.10"
     hooks:
       - id: ruff
         args: ["--fix"]
       - id: ruff-format
   - repo: https://github.com/PyCQA/isort
-    rev: 6.0.1
+    rev: 7.0.0
     hooks:
       - id: isort
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunkit_spex/extern)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-ast
       - id: check-case-conflict

.rtd-environment.yml

@@ -2,7 +2,6 @@ name: sunkit-spex
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.13
   - pip
   - graphviz!=2.42.*,!=2.43.*
-  - sqlite<3.49.0

.ruff.toml

@@ -36,8 +36,6 @@ select = [
 extend-ignore = [
   # pycodestyle (E, W)
   "E501", # ignore line length will use a formatter instead
-  # pyupgrade (UP)
-  "UP038", # Use | in isinstance - not compatible with models and is slower
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT023", # Always use () on pytest decorators

changelog/234.breaking.rst

@@ -0,0 +1,9 @@
+Bump minimum python version to 3.12 and also update some dependencies:
+* matplotlib>=3.9
+* numdifftools>=0.9.42
+* numpy>=1.26
+* parfive>=2.1
+* scipy>=1.12
+* sunpy>=7.0
+* xarray>=2023.12
+* ndcube>=2.3

pyproject.toml

@@ -9,25 +9,25 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "sunkit_spex"
 description = "A package for solar X-ray spectroscopy."
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 readme = { file = "README.rst", content-type = "text/x-rst" }
-license = { file = "licenses/LICENSE.rst" }
+license-files = ["licenses/LICENSE.rst"]
 authors = [
   { name = "The SunPy Community", email = "[email protected]" },
 ]
 dependencies = [
     "corner>=2.2",
     "emcee>=3.1",
-    "matplotlib>=3.7",
+    "matplotlib>=3.9",
     "nestle>=0.2",
-    "numdifftools>=0.9.40",
-    "numpy>=1.24",
-    "parfive>=2.0",
-    "scipy>=1.11",
-    "sunpy>=6.0",
-    "xarray>=2022.10",
+    "numdifftools>=0.9.42",
+    "numpy>=1.26",  # Note: keeping support for numpy 1.x for now
+    "parfive>=2.1",
+    "scipy>=1.12",
+    "sunpy>=7.0",
+    "xarray>=2023.12",
     "gwcs>=0.21.0",
-    "ndcube>=2.1",
+    "ndcube>=2.3",
 ]
 
 dynamic = ["version"]

pytest.ini

@@ -40,3 +40,6 @@ filterwarnings =
     # Oldestdeps issues
     ignore:`finfo.machar` is deprecated:DeprecationWarning
     ignore:Please use `convolve1d` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.:DeprecationWarning
+    ignore::pyparsing.warnings.PyparsingDeprecationWarning
+    ignore::FutureWarning:arviz.*
+    ignore:The isiterable function.*:astropy.utils.exceptions.AstropyDeprecationWarning

sunkit_spex/models/physical/tests/test_thermal.py

@@ -388,7 +388,7 @@ def chianti_kev_lines_Fe2():
 
 @pytest.mark.parametrize("ssw", [fvth_simple, fvth_Fe2])
 def test_thermal_emission_against_ssw(ssw):
-    input_args, input_args_class, energy_edges, expected = ssw()
+    _, input_args_class, energy_edges, expected = ssw()
     model_class = thermal.ThermalEmission(*input_args_class)
     output_class = model_class(energy_edges)
     expected_value = expected.to_value(output_class.unit)
@@ -397,7 +397,7 @@ def test_thermal_emission_against_ssw(ssw):
 
 @pytest.mark.parametrize("ssw", [chianti_kev_cont_simple, chianti_kev_cont_Fe2])
 def test_continuum_emission_against_ssw(ssw):
-    input_args, input_args_class, energy_edges, expected = ssw()
+    _, input_args_class, energy_edges, expected = ssw()
     model_class = thermal.ContinuumEmission(*input_args_class)
     output_class = model_class(energy_edges)
     expected_value = expected.to_value(output_class.unit)
@@ -406,7 +406,7 @@ def test_continuum_emission_against_ssw(ssw):
 
 @pytest.mark.parametrize("ssw", [chianti_kev_lines_simple, chianti_kev_lines_Fe2])
 def test_line_emission_against_ssw(ssw):
-    input_args, input_args_class, energy_edges, expected = ssw()
+    _, input_args_class, energy_edges, expected = ssw()
     model_class = thermal.LineEmission(*input_args_class)
     output_class = model_class(energy_edges)
     expected_value = expected.to_value(output_class.unit)
@@ -426,7 +426,7 @@ def test_len1_energy_input():
 def test_energy_out_of_range_error():
     with pytest.raises(
         ValueError,
-        match="Lower bound of the input energy must be within the range 1.0002920302956426--10.34753795157738 keV. ",
+        match=r"Lower bound of the input energy must be within the range 1.0002920302956426--10.34753795157738 keV. ",
     ):
         thermal.ThermalEmission(6 * u.MK, 1e-5 / u.cm**3)([0.01, 10] * u.keV)
 
@@ -448,7 +448,7 @@ def test_line_energy_out_of_range_warning():
 def test_continuum_energy_out_of_range():
     with pytest.raises(
         ValueError,
-        match="Lower bound of the input energy must be within the range 1.0009873438468269--200.15819869050395 keV.",
+        match=r"Lower bound of the input energy must be within the range 1.0009873438468269--200.15819869050395 keV.",
     ):
         # Use an energy range that goes out of bounds
         # on the lower end--should error