switch to uv

.github/workflows/python-package.yml

@@ -16,31 +16,25 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: s-weigand/setup-conda@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v5
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
+
+    - name: Setup venv
+      run: uv python install
+
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 coverage psutil requests kaleido
-        python -m pip install -r requirements.txt
-        python -m pip install -r test-requirements.txt
-        python -m pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      run: uv sync --all-extras --dev
+
     - name: Test with pytest
       run: |
-        coverage run -m pytest --disable-warnings -p no:warnings test
+        uv run python -m coverage run -m pytest -v --disable-warnings -p no:warnings test
     - name: Generate Coveralls reports
       if: startsWith(matrix.os, 'ubuntu')
       uses: AndreMiras/coveralls-python-action@develop

.pre-commit-config.yaml

@@ -1,12 +1,4 @@
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-    - id: black
-      language_version: python3
-      args: # arguments to configure black
-        - --line-length=79
-
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -23,20 +15,12 @@ repos:
     - id: debug-statements
     - id: requirements-txt-fixer
 
--   repo: local
-    hooks:
-    - id: remarklint
-      name: remarklint
-      language: node
-      entry: remark
-      types: [markdown]
-      args: ["--frail", "--quiet"]
-      additional_dependencies:
-        [
-          remark,
-          remark-lint,
-          remark-cli,
-          remark-preset-lint-recommended,
-          remark-lint-list-item-indent,
-          remark-lint-no-undefined-references,
-        ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.14.0
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

calibration_test.ipynb

@@ -8,7 +8,6 @@
    "source": [
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "import astropy.units as u\n",
     "from astropy.io import fits\n",
     "from scipy.signal import find_peaks\n",
     "from rascal.calibrator import Calibrator\n",
@@ -51,19 +50,16 @@
     }
    ],
    "source": [
-    "spectrum = np.median(fits.open('./examples/v_a_20190516_55_1_0_1.fits')[0].data[110:120], axis=0)\n",
+    "spectrum = np.median(fits.open(\"./examples/v_a_20190516_55_1_0_1.fits\")[0].data[110:120], axis=0)\n",
     "print(spectrum.shape)\n",
     "\n",
-    "resampled_flux = resample(spectrum-spectrum.min(), len(spectrum)*4)\n",
+    "resampled_flux = resample(spectrum - spectrum.min(), len(spectrum) * 4)\n",
     "peaks, _ = find_peaks(resampled_flux, prominence=150, distance=20, threshold=None)\n",
     "peaks = peaks / 4.0\n",
     "\n",
-    "plt.figure(figsize=(18,3))\n",
+    "plt.figure(figsize=(18, 3))\n",
     "plt.plot(spectrum)\n",
-    "plt.vlines(peaks,\n",
-    "              spectrum[peaks.astype('int')],\n",
-    "              spectrum.max(),\n",
-    "              colors='C1')"
+    "plt.vlines(peaks, spectrum[peaks.astype(\"int\")], spectrum.max(), colors=\"C1\")"
    ]
   },
   {
@@ -72,10 +68,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "c = Calibrator(peaks, elements=[\"Xe_strong\"],\n",
-    "               min_wavelength=3400.,\n",
-    "               max_wavelength=8100.,\n",
-    "               range_tolerance=200)\n",
+    "c = Calibrator(peaks, elements=[\"Xe_strong\"], min_wavelength=3400.0, max_wavelength=8100.0, range_tolerance=200)\n",
     "c.set_fit_constraints(n_pix=len(spectrum))"
    ]
   },
@@ -155,10 +148,10 @@
     }
    ],
    "source": [
-    "peaks, wavelengths, lamps = np.loadtxt(\"./examples/ground_truth_v_a.csv\", delimiter=',', dtype='U').T\n",
+    "peaks, wavelengths, lamps = np.loadtxt(\"./examples/ground_truth_v_a.csv\", delimiter=\",\", dtype=\"U\").T\n",
     "\n",
-    "peaks = peaks.astype('float32')\n",
-    "wavelengths = wavelengths.astype('float32')\n",
+    "peaks = peaks.astype(\"float32\")\n",
+    "wavelengths = wavelengths.astype(\"float32\")\n",
     "\n",
     "x, y = c._combine_linear_estimates(c.candidates)\n",
     "plt.scatter(x, y, s=20, label=\"Candidate match\")\n",

docs/source/conf.py

@@ -92,6 +92,6 @@
         html_theme = "sphinx_rtd_theme"
         html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
         # html_static_path = ["_static"]
-    except:
+    except: #noqa E722
         html_theme = "alabaster"
         # html_static_path = ["_static"]

docs/source/thresh_plot.py

@@ -6,9 +6,7 @@
 # data point
 pix = np.arange(0, 1001, 50)
 wave = 4000.0 + pix**0.63437 * 50.0
-plt.scatter(
-    pix, wave, label="Solution", c="midnightblue", s=10, marker="x", zorder=15
-)
+plt.scatter(pix, wave, label="Solution", c="midnightblue", s=10, marker="x", zorder=15)
 
 # minmax & range tolerance
 wave_min = 4000.0
@@ -29,9 +27,7 @@
     lw=1,
     c="orangered",
 )
-plt.plot(
-    [pix[0], pix[-1]], [wave_min, wave_min], c="orangered", lw=1, label=""
-)
+plt.plot([pix[0], pix[-1]], [wave_min, wave_min], c="orangered", lw=1, label="")
 plt.plot(
     [pix[0], pix[-1]],
     [wave_max - range_tolerance, wave_max - range_tolerance],
@@ -47,9 +43,7 @@
     lw=1,
     c="orangered",
 )
-plt.plot(
-    [pix[0], pix[-1]], [wave_max, wave_max], c="orangered", lw=1, label=""
-)
+plt.plot([pix[0], pix[-1]], [wave_max, wave_max], c="orangered", lw=1, label="")
 
 plt.annotate(
     s="",