Scientiric Python Guide

icecube · Jan 25, 2024 · 067c40b · 067c40b
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,22 @@
+# SPDX-FileCopyrightText: © 2024 the i3astropy contributors
+#
+# SPDX-License-Identifier: BSD-2-Clause
+
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      actions:
+        patterns:
+          - "*"
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -6,49 +6,53 @@ name: Tests
 on:
   push:
     branches:
-    - main
+      - main
   pull_request:
+  workflow_dispatch:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   Tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [ubuntu-22.04]
         include:
-        - python-version: 3.12
-          os: macos-12
+          - python-version: 3.12
+            os: macos-12
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: pip
-        cache-dependency-path: pyproject.toml
-    - name: Install i3astropy
-      run: python3 -m pip install .[test]
-    - name: Run Unit Tests
-      run: pytest
-    - name: Upload Coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        fail_ci_if_error: false
-        verbose: true
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install i3astropy
+        run: python3 -m pip install .[test]
+      - name: Run Unit Tests
+        run: pytest
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: false
+          verbose: true
   Docs:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-        cache: pip
-        cache-dependency-path: pyproject.toml
-    - name: Install i3astropy
-      run: python3 -m pip install .[docs]
-    - name: Build Docs
-      run: mkdocs build
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install i3astropy
+        run: python3 -m pip install .[docs]
+      - name: Build Docs
+        run: mkdocs build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,67 +6,77 @@ ci:
   autoupdate_commit_msg: autoupdate pre-commit hooks
   autoupdate_schedule: quarterly
 repos:
-- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.12.0
-  hooks:
-  - id: pretty-format-toml
-    args: [--autofix]
-  - id: pretty-format-yaml
-    args: [--autofix]
-- repo: https://github.com/fsfe/reuse-tool
-  rev: v2.1.0
-  hooks:
-  - id: reuse
-- repo: https://github.com/psf/black
-  rev: 23.12.1
-  hooks:
-  - id: black
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.9
-  hooks:
-  - id: ruff
-    args: [--fix]
-- repo: https://github.com/pycqa/pylint
-  rev: v3.0.3
-  hooks:
-  - id: pylint
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
-  hooks:
-  - id: codespell
-    args: [-L, livetime]
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
-  hooks:
-  - id: python-check-blanket-noqa
-  - id: python-no-log-warn
-  - id: python-no-eval
-  - id: python-use-type-annotations
-- repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.5.4
-  hooks:
-  - id: forbid-crlf
-  - id: forbid-tabs
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
-  hooks:
-  - id: check-added-large-files
-  - id: check-ast
-  - id: check-builtin-literals
-  - id: check-case-conflict
-  - id: check-docstring-first
-  - id: check-executables-have-shebangs
-  - id: check-merge-conflict
-  - id: check-shebang-scripts-are-executable
-  - id: check-toml
-  - id: check-vcs-permalinks
-  - id: check-yaml
-  - id: debug-statements
-  - id: detect-private-key
-  - id: end-of-file-fixer
-  - id: fix-byte-order-marker
-  - id: mixed-line-ending
-  - id: name-tests-test
-    args: [--pytest-test-first]
-  - id: trailing-whitespace
-    exclude: \.svg$
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        files: \.ya?ml$
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.12.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix]
+  - repo: https://github.com/fsfe/reuse-tool
+    rev: v3.0.1
+    hooks:
+      - id: reuse
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [numpy]
+        files: src/i3astropy
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.14
+    hooks:
+      - id: ruff
+        args: [--fix, --show-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pycqa/pylint
+    rev: v3.0.3
+    hooks:
+      - id: pylint
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        args: [-L, livetime]
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-no-log-warn
+      - id: python-no-eval
+      - id: python-use-type-annotations
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.4
+    hooks:
+      - id: forbid-crlf
+      - id: forbid-tabs
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: [--pytest-test-first]
+      - id: trailing-whitespace
+        exclude: \.svg$
diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ so that you can test changes without reinstalling the module:
 This example takes an event which occurred at DAQ time (2021, 155525688461058500) and was reconstructed in the direction of zenith = 0.73884 rad, azimuth = 2.7348 rad and converts it to RA and Dec.
 In addition, get the Sun position in IceCube coordinates at the same time.
 
-```python
+```pycon
 
 >>> from astropy.coordinates import ICRS, get_sun
 >>> from astropy.time import Time

diff --git a/examples/compare_ps_sample.py b/examples/compare_ps_sample.py
@@ -17,9 +17,10 @@
 from astropy import units as u
 from astropy.coordinates import ICRS
 from astropy.time import Time
-from i3astropy import I3Dir
 from numpy import allclose
 
+from i3astropy import I3Dir
+
 # need file from /data/ana/analyses/ps_tracks/version-004-p00/IC86_2019_exp.npy
 f = np.load("IC86_2019_exp.npy")
 N = 10000

diff --git a/examples/plot_analemma.py b/examples/plot_analemma.py
@@ -16,9 +16,10 @@
 from astropy.coordinates import get_sun
 from astropy.time import Time
 from astropy.units import day
-from i3astropy import I3Dir
 from matplotlib import ticker
 
+from i3astropy import I3Dir
+
 LEFT_MARGIN, RIGHT_MARGIN = 0.08, 0.02
 ANALAMA_WIDTH = 0.2
 TOP_MARGIN, BOTTOM_MARGIN = 0.01, 0.08

diff --git a/examples/plot_moon.py b/examples/plot_moon.py
@@ -18,10 +18,11 @@
 from astropy.coordinates import get_moon
 from astropy.time import Time
 from astropy.units import day
-from i3astropy import I3Dir
 from matplotlib.dates import DateFormatter, YearLocator
 from matplotlib.ticker import FormatStrFormatter
 
+from i3astropy import I3Dir
+
 warnings.simplefilter("ignore")
 
 t0 = Time("2020-01-02 00:00")

diff --git a/examples/plot_sun_azimuth.py b/examples/plot_sun_azimuth.py
@@ -18,9 +18,10 @@
 from astropy.coordinates import ICRS, get_sun
 from astropy.time import Time
 from astropy.units import day, deg
-from i3astropy import I3Dir
 from matplotlib import patches, ticker
 
+from i3astropy import I3Dir
+
 
 # pylint: disable=R0913
 def draw_circ(axis, radius, cent_x, cent_y, angle_, theta2_, color_="black"):

diff --git a/pyproject.toml b/pyproject.toml
@@ -52,33 +52,55 @@ line_length = 108
 multi_line_output = 3
 use_parentheses = true
 
+[tool.mypy]
+allow_subclassing_any = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+exclude = 'docs|examples|tests'
+files = 'src/i3astropy'
+ignore_missing_imports = true
+plugins = "numpy.typing.mypy_plugin"
+strict = true
+warn_unreachable = true
+
 [tool.pylint.format]
 max-line-length = "108"
 
 [tool.pylint.messages_control]
 disable = ["W0201", "R0903", "E0401", "C0411"]
 
 [tool.pytest.ini_options]
-addopts = "--cov=i3astropy --doctest-glob='README.md'"
+addopts = ["--cov=i3astropy", "--doctest-glob=README.md", "-ra", "--strict-config", "--strict-markers"]
+filterwarnings = ["error"]
+log_cli_level = "INFO"
+minversion = 7
 testpaths = ["tests", "README.md"]
+xfail_strict = true
 
 [tool.ruff]
+line-length = 108
+show-fixes = true
+src = ['src']
+target-version = "py39"
+
+[tool.ruff.lint]
 fixable = ["I"]
 ignore = [
-  "ANN",  # flake8-annotations
+  "ANN401",  # any-type
   "INP001",  # flake8-no-pep420
   "S101",  # assert-used
   "D213",  # multi-line-summary-second-line incompatible with multi-line-summary-first-line
   "D203",  # one-blank-line-before-class" incompatible with no-blank-line-before-class
   "RUF012"  # mutable-class-default
 ]
-line-length = 108
 select = ["ALL"]
-target-version = "py39"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "examples/*" = [
+  "ANN",  # flake8-annotations
   "PLR",  # max-statements
   "ARG",  # flake8-unused-arguments
   "T201"  # flake8-print
 ]
+"tests/*" = [
+  "ANN"  # flake8-annotations
+]