Building docs on Read the Docs, adding pre-commit formatting (#219)

Author: dfm

.cirrus.yml

@@ -5,7 +5,7 @@ cirrus_wheels_macos_arm64_task:
     PATH: /opt/homebrew/opt/python@3.10/bin:$PATH
     CIBW_ENVIRONMENT: >
       MACOSX_DEPLOYMENT_TARGET=12.0
-      _PYTHON_HOST_PLATFORM="macosx-12.0-arm64"    
+      _PYTHON_HOST_PLATFORM="macosx-12.0-arm64"
       SPS_HOME="${CIRRUS_WORKING_DIR}/src/fsps/libfsps"
     PKG_CONFIG_PATH: /opt/arm64-builds/lib/pkgconfig
     CMAKE_PREFIX_PATH: /opt/arm64-builds/

.github/workflows/build_docs.sh

@@ -1,10 +1,18 @@
 name: Release
 on:
-  release:
-    types: [published]
   push:
-    branches: [main]
-  pull_request:
+    branches:
+      - main
+    tags:
+      - "*"
+  # pull_request:
+  workflow_dispatch:
+    inputs:
+      prerelease:
+        description: "Run a pre-release, testing the build"
+        required: false
+        type: boolean
+        default: false
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -17,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: 
+        os:
           - "ubuntu-latest"
           - "macos-latest"
           # - "windows-latest"
@@ -64,20 +72,27 @@ jobs:
         with:
           task: cirrus_wheels_macos_arm64
           commit: ${{ github.event.pull_request.head.sha || github.sha }}
-        timeout-minutes: 15  
+        timeout-minutes: 15
       - run: ls dist
 
-  upload_pypi:
+  publish:
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fsps
+    permissions:
+      id-token: write
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
+      - name: Get macOS arm64 wheels from Cirrus CI
+        uses: getsentry/action-wait-for-cirrus@v1.0.0
+        with:
+          task: cirrus_wheels_macos_arm64
+          commit: ${{ github.event.pull_request.head.sha || github.sha }}
+        timeout-minutes: 15
       - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
       - uses: pypa/gh-action-pypi-publish@v1.8.7
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
-          # To test: repository_url: https://test.pypi.org/legacy/

.github/workflows/release.yml

@@ -70,28 +70,3 @@ jobs:
         run: python -m nox --non-interactive --no-error-on-missing-interpreters -s ${{ matrix.nox-session }}-${{ matrix.python-version }}
         env:
           SPS_HOME: ${{ github.workspace }}/src/fsps/libfsps
-  
-  docs:
-    if: github.event_name != 'pull_request'
-    name: "docs"
-    runs-on: ubuntu-latest
-    steps:
-      - name: Clone the repo
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-          submodules: recursive
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip sphinx
-          python -m pip install .
-      - name: Build documentation
-        run: .github/workflows/build_docs.sh
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          SPS_HOME: ${{ github.workspace }}/src/fsps/libfsps
-          STABLE: ${{ github.event_name == 'release' && github.event.action == 'published' }}

.github/workflows/tests.yml

@@ -12,10 +12,10 @@ jobs:
         with:
           submodules: true
           fetch-depth: 0
-      
+
       - name: Update the submodule
         run: git submodule foreach git pull origin master
-      
+
       - name: Create a PR
         uses: peter-evans/create-pull-request@v5
         with:
@@ -25,5 +25,5 @@ jobs:
           title: Updating FSPS
           body: |
             Automatically updating the FSPS submodule
-            
+
             **Maintainers should close and then re-open this PR to get the tests to run.**

.github/workflows/update-fsps.yml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude_types: [json, binary]
+      - id: check-yaml
+  - repo: https://github.com/psf/black
+    rev: "23.1.0"
+    hooks:
+      - id: black-jupyter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.0.277"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ find_package(
 
 # Find the f2py headers
 execute_process(
-  COMMAND "${PYTHON_EXECUTABLE}" 
+  COMMAND "${PYTHON_EXECUTABLE}"
           "${CMAKE_CURRENT_SOURCE_DIR}/tools/f2py_include.py"
   OUTPUT_VARIABLE F2PY_INCLUDE_DIR
   OUTPUT_STRIP_TRAILING_WHITESPACE)

CMakeLists.txt

@@ -1,4 +1,4 @@
-Copyright 2013-2021 Python-FSPS developers.
+Copyright 2013-2023 Python-FSPS developers.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

LICENSE.rst

@@ -1,25 +1,24 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import (division, print_function, absolute_import,
-                        unicode_literals)
-import pyfits
-import numpy as np
+from __future__ import absolute_import, division, print_function, unicode_literals
+
 import matplotlib.pyplot as pl
+import numpy as np
+import pyfits
+
 import fsps
 
 # Measurements of cluster parameters.
-tage = 10. ** (8.04 - 9)
+tage = 10.0 ** (8.04 - 9)
 logmass = 4.09
 dist_mod = 24.5
 
 # Set up the stellar population model.
 sp = fsps.StellarPopulation(imf_type=2, dust_type=1, mwr=3.1, dust2=0.3)
 
 # The measured magnitudes from the literature.
-data = {"wfc3_f160w": 16.386,
-        "wfc3_f275w": 17.398,
-        "wfc_acs_f814w": 17.155}
+data = {"wfc3_f160w": 16.386, "wfc3_f275w": 17.398, "wfc_acs_f814w": 17.155}
 
 # There are also a few filters that we have data for but aren't included in
 # the standard FSPS install:
@@ -39,15 +38,14 @@
 
 # Compute the model magnitudes.
 for b, v in data.iteritems():
-    print(b, v, sp.get_mags(zmet=20, tage=tage, band=b) - 2.5 * logmass
-          + dist_mod)
+    print(b, v, sp.get_mags(zmet=20, tage=tage, band=b) - 2.5 * logmass + dist_mod)
 
 # Compute the model spectrum in ``L_sun / A``.
 lam, spec = sp.get_spectrum(zmet=20, tage=tage, peraa=True)
-spec *= 3.839e33 * 10. ** (logmass - dist_mod / 2.5)
+spec *= 3.839e33 * 10.0 ** (logmass - dist_mod / 2.5)
 
 f = 1.0  # obs_spec[0, obs_lambda < 5000.][-1] / spec[lam < 5000.][-1]
-print(obs_spec[0, obs_lambda < 5000.][-1] / spec[lam < 5000.][-1])
+print(obs_spec[0, obs_lambda < 5000.0][-1] / spec[lam < 5000.0][-1])
 
 pl.loglog(obs_lambda, obs_spec[0], "k")
 pl.loglog(lam, spec * f, "r")

demos/dao69.py

@@ -7,7 +7,7 @@
 """
 
 import os
-import numpy as np
+
 import matplotlib.pyplot as pl
 from matplotlib.backends.backend_pdf import PdfPages
 
@@ -18,19 +18,19 @@ def makefig(sps, tage=13.7, oldspec=None, **plotkwargs):
     w, spec = sps.get_spectrum(tage=tage)
     fig, ax = pl.subplots()
     if oldspec is not None:
-        ax.plot(w, oldspec / w * 1e19, color='gray', linewidth=2, alpha=0.5)
-    ax.plot(w, spec / w * 1e19, 'C2', linewidth=2)
+        ax.plot(w, oldspec / w * 1e19, color="gray", linewidth=2, alpha=0.5)
+    ax.plot(w, spec / w * 1e19, "C2", linewidth=2)
     return fig, ax, spec
 
 
 def prettify(fig, ax, label=None):
     ax.set_xlim(0.9e3, 1e6)
-    ax.set_xscale('log')
+    ax.set_xscale("log")
     ax.set_ylim(0.01, 2)
-    #ax.set_yscale('log')
-    ax.set_xlabel(r'rest-frame $\lambda$ ($\AA$)', fontsize=20)
-    ax.set_ylabel(r'$\lambda \, f_\lambda$', fontsize=20)
-    ax.tick_params(axis='both', which='major', labelsize=16)
+    # ax.set_yscale('log')
+    ax.set_xlabel(r"rest-frame $\lambda$ ($\AA$)", fontsize=20)
+    ax.set_ylabel(r"$\lambda \, f_\lambda$", fontsize=20)
+    ax.tick_params(axis="both", which="major", labelsize=16)
     if label is not None:
         ax.text(0.63, 0.85, label, transform=ax.transAxes, fontsize=16)
 
@@ -39,94 +39,93 @@ def prettify(fig, ax, label=None):
 
 
 if __name__ == "__main__":
-
-    pl.rc('text', usetex=True)
-    pl.rc('font', family='serif')
-    pl.rc('axes', grid=False)
-    pl.rc('xtick', direction='in')
-    pl.rc('ytick', direction='in')
-    pl.rc('xtick', top=True)
-    pl.rc('ytick', right=True)
+    pl.rc("text", usetex=True)
+    pl.rc("font", family="serif")
+    pl.rc("axes", grid=False)
+    pl.rc("xtick", direction="in")
+    pl.rc("ytick", direction="in")
+    pl.rc("xtick", top=True)
+    pl.rc("ytick", right=True)
 
     sps = fsps.StellarPopulation(zcontinuous=1)
     ilib, slib, dlib = sps.libraries
     print(ilib, slib)
     os.makedirs("./figures", exist_ok=True)
-    pdf = PdfPages('./figures/features.pdf')
+    pdf = PdfPages("./figures/features.pdf")
 
     # Basic spectrum
-    sps.params['sfh'] = 4
-    sps.params['tau'] = 5.0
-    sps.params['logzsol'] = 0.0
-    sps.params['dust_type'] = 4  # kriek and Conroy
-    sps.params['imf_type'] = 2  # kroupa
-    sps.params['imf3'] = 2.3
+    sps.params["sfh"] = 4
+    sps.params["tau"] = 5.0
+    sps.params["logzsol"] = 0.0
+    sps.params["dust_type"] = 4  # kriek and Conroy
+    sps.params["imf_type"] = 2  # kroupa
+    sps.params["imf3"] = 2.3
     fig, ax, spec = makefig(sps)
     fig, ax = prettify(fig, ax, label=r"$\tau=5$, Age$=13.7$,\\n$\log Z/Z_\odot=0.0$")
     pdf.savefig(fig)
     pl.close(fig)
 
     # change IMF
-    sps.params['imf3'] = 2.5
+    sps.params["imf3"] = 2.5
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"IMF slope")
     pdf.savefig(fig)
 
     # Attenuate
-    sps.params['add_dust_emission'] = False
-    sps.params['dust2'] = 0.2
+    sps.params["add_dust_emission"] = False
+    sps.params["dust2"] = 0.2
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"Dust Attenuation")
     pdf.savefig(fig)
     pl.close(fig)
 
     # Dust emission
-    sps.params['add_dust_emission'] = True
+    sps.params["add_dust_emission"] = True
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"Dust Emission")
     pdf.savefig(fig)
     pl.close(fig)
 
     # Dust temperature
-    sps.params['duste_umin'] = 10
+    sps.params["duste_umin"] = 10
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"Dust SED\\n({})".format(dlib))
     pdf.savefig(fig)
     pl.close(fig)
 
     # AGN emission
-    sps.params['fagn'] = 0.3
+    sps.params["fagn"] = 0.3
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"AGN dust\\n(Nenkova)")
     pdf.savefig(fig)
     pl.close(fig)
 
     # Nebular emission
-    sps.params['add_neb_emission'] = True
-    sps.params['gas_logu'] = -3.5
+    sps.params["add_neb_emission"] = True
+    sps.params["gas_logu"] = -3.5
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"Neb. emission\\n(Byler)")
     pdf.savefig(fig)
     pl.close(fig)
 
     # change logu
-    sps.params['gas_logu'] = -1.0
+    sps.params["gas_logu"] = -1.0
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"Change U$_{neb}$")
     pdf.savefig(fig)
     pl.close(fig)
 
     # change logz
-    sps.params['logzsol'] = -0.5
-    sps.params['gas_logz'] = -0.5
+    sps.params["logzsol"] = -0.5
+    sps.params["gas_logz"] = -0.5
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"$\log Z/Z_\odot=-0.5$")
     pdf.savefig(fig)
     pl.close(fig)
 
     # IGM absorption
-    sps.params['zred'] = 6.0
-    sps.params['add_igm_absorption'] = True
+    sps.params["zred"] = 6.0
+    sps.params["add_igm_absorption"] = True
     fig, ax, spec = makefig(sps, oldspec=spec)
     fig, ax = prettify(fig, ax, label=r"IGM attenuation\\n(Madau, $z=6$)")
     pdf.savefig(fig)