bbf 0.6.0__tar.gz

bbf-0.6.0/.gitattributes

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+*.parquet filter=lfs diff=lfs merge=lfs -text

bbf-0.6.0/.gitignore

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+.DS_Store
+.idea
+*.log
+tmp/
+*.ipynb_checkpoints*
+build/
+dist/
+**__pycache__
+*.so
+*.egg-info
+*~
+.pytest_cache
+.cache
+.coverage
+.gitlab-ci-local/
+dev.py

bbf-0.6.0/.gitlab-ci.yml

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+# Adapted from https://docs.gitlab.com/ee/ci/caching/#cache-python-dependencies.
+default:
+  image: python:3.12
+  before_script:
+    - apt update
+    - apt install -y build-essential git libhdf5-dev libsuitesparse-dev
+    # We need numpy<2 because of extinction package compiled on numpy-1.*
+    - pip install "numpy<2" git+https://github.com/nregnault/sncosmo
+    # TODO(mbernard) this is a dirty fix while
+    # https://github.com/sncosmo/sncosmo/pull/400 is not merged
+    - pip install git+https://gitlab.in2p3.fr/lemaitre/bandpasses.git@v0.4.0
+
+
+test-gcc:
+  image: "python:$VERSION"
+  stage: test
+  script:
+    - VERBOSE=1 CXX=g++ pip install -v .[test,gaia]
+    - pytest -v
+  parallel:
+    matrix:
+      - VERSION: ['3.9', '3.10', '3.11', '3.12']
+
+
+# do not test on several Python versions here, we just want to be sure the bbf
+# C/C++ extension can be compiled with clang
+test-clang:
+  stage: test
+  script:
+    - apt install -y clang libomp-dev
+    - VERBOSE=1 CXX=clang++ pip install -v .[test,gaia]
+    - pytest -v
+
+
+sdist:
+  stage: deploy
+  script:
+    - pip install build
+    - python -m build --sdist --outdir dist
+  artifacts:
+    paths:
+      - dist/*.tar.gz
+
+
+pypi:
+  # publish the source distribution on https://pypi.org/project/bbf/, only when
+  # a new tag
+  stage: deploy
+  needs: ["sdist"]
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - pip install twine
+    - twine upload --non-interactive --repository pypi dist/*

bbf-0.6.0/CHANGELOG.md

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+# Changelog
+
+This documents the changes in `bbf` releases. Version numbers follows [semantic
+versioning](https://semver.org/).
+
+
+## bbf-0.6.0
+
+* Added `bbf.atmosphere` module to load atosphere extinction models.
+* Ensure compatibility with future version of `sncosmo` (normalized a call to
+  `sncosmo.get_bandpass`).
+* `gaiaxpy` becomes a standard dependency, installed by default.
+* add `__contains__` method to SNFilterSet
+* If a static bandbass is requested and not in the filterlib, fetch it from sncosmo
+* Extended default wavelength range of SNFilterSet basis to [2000,11000]
+
+
+## bbf-0.5.2
+
+`gaiaxpy` is now an optionnal dependency, install it with `pip install
+bbf[gaia]` or a separate `pip install gaiaxpy`. See
+[#17](https://gitlab.in2p3.fr/lemaitre/bbf/-/issues/17)
+
+
+## bbf-0.5.1
+
+* Fixed a regression introduced in `bbf-0.5.0` (removed
+  `bspline.Bspline{2D}.__eq__` method making the class unhashable)
+
+
+## bbf-0.5.0
+
+* Incompatible with `python-3.13`. See
+    [#16](https://gitlab.in2p3.fr/lemaitre/bbf/-/issues/16)
+* Added `bbf.stellarlib.gaia`
+* Fixed a bug when using `CompositeBandpass` without specifying a `sensor_id`
+  (issue 15).
+* Removed useless parameter in `bspline.lgram`
+* Deprecated property `BSpline.nj` and `BSpline2D.nj`, use `__len__` instead.
+* Code cleanup (PEP8)
+
+
+## bbf-0.4.0
+
+* Added a `filterlib.CompositeBandpasses` class to simplifies the management of
+  bandpasses that depends on the `sensor_id`.
+* Comes with some simplifications in Filterlib and FluxArgs.
+
+
+## bbf-0.3.2
+
+Fix several regressions introduced in `bbf-0.3.0`
+
+* `BSpline` instances can be pickled
+* Sparse matrices returned by `BSpline` instances are `csr_matrix` (was `csr_array`)
+* Reintroduction of `BSpline.nj`
+
+
+## bbf-0.3.1
+
+* Bugfixes
+
+  * Fixed a bug with `OpenMP` instructions in C code. The bug impacted the
+    `clang` compiler while `gcc` compiled code was fine.
+
+
+## bbf-0.3.0
+
+* Improvments
+
+  * Uses `nanobind` instead of `ctypes` to wrap the bsplines C extension. This
+    allows for a simple cross-platforms installation of the package. See
+    [#6](https://gitlab.in2p3.fr/lemaitre/bbf/-/issues/6).
+  * Few unit tests (about bsplines) under continuous integration.
+
+
+## bbf-0.2.0
+
+First public release.

bbf-0.6.0/CMakeLists.txt

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+# This CMake file is meant to be executed using 'scikit-build'. Running it
+# directly will almost certainly not produce the desired result. If you are a
+# user trying to install this package, please use the command below, which will
+# install all necessary build dependencies, compile the package in an isolated
+# environment, and then install it.
+# =====================================================================
+# $ pip install .
+# =====================================================================
+# If you are a software developer, and this is your own package, then it is
+# usually much more efficient to install the build dependencies in your
+# environment once and use the following command that avoids a costly creation
+# of a new virtual environment at every compilation:
+# =====================================================================
+# $ pip install nanobind ninja scikit-build-core[pyproject]
+# $ pip install --no-build-isolation -ve .
+# =====================================================================
+# You may optionally add -Ceditable.rebuild=true to auto-rebuild when the
+# package is imported. Otherwise, you need to re-run the above after editing C++
+# files.
+
+cmake_minimum_required(VERSION 3.18)
+
+# The project name is imported from pyproject.toml
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+# Release build (optimized for speed) by default
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+# Find the required dependencies to build the extension
+find_package(Python 3.9 REQUIRED COMPONENTS Interpreter Development.Module ${SKBUILD_SABI_COMPONENT})
+find_package(nanobind CONFIG REQUIRED)
+find_package(OpenMP REQUIRED)
+
+# The nanobind extension wrapping the bspline.hpp code into Python
+nanobind_add_module(bspline_ext STABLE_ABI NB_STATIC NOMINSIZE LTO bbf/bspline/src/bspline_ext.cpp)
+install(TARGETS bspline_ext LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+target_link_libraries(bspline_ext PUBLIC OpenMP::OpenMP_CXX)

bbf-0.6.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Nicolas Regnault
+
+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 the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bbf-0.6.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: bbf
+Version: 0.6.0
+Summary: Fast computation of broadband fluxes and magnitudes
+Keywords: astronomy,astrophysics
+Author-Email: Nicolas Regnault <nicolas.regnault@lpnhe.in2p3.fr>
+License: MIT License
+        
+        Copyright (c) 2024 Nicolas Regnault
+        
+        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 the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Project-URL: Homepage, https://gitlab.in2p3.fr/lemaitre/bbf
+Project-URL: Repository, https://gitlab.in2p3.fr/lemaitre/bbf
+Project-URL: Changelog, https://gitlab.in2p3.fr/lemaitre/bbf/-/blob/main/CHANGELOG.md
+Requires-Python: >=3.9
+Requires-Dist: astropy
+Requires-Dist: astroquery
+Requires-Dist: fastparquet
+Requires-Dist: gaiaxpy
+Requires-Dist: getCalspec
+Requires-Dist: healpy
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: platformdirs
+Requires-Dist: pyifu
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-sparse
+Requires-Dist: sncosmo
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: lemaitre-bandpasses>=0.3.3; extra == "test"
+Provides-Extra: test
+Description-Content-Type: text/markdown
+
+# Broadband fluxes (`bbf`)
+
+[![PyPI - Version](https://img.shields.io/pypi/v/bbf.svg)](https://pypi.org/project/bbf)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/bbf.svg)](https://anaconda.org/conda-forge/bbf)
+[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/bbf.svg)](https://anaconda.org/conda-forge/bbf)
+
+-----
+
+**Table of contents**
+- [Installation](#installation)
+- [Getting started](#getting started)
+- [License](#license)
+
+A module to evaluate the broadband fluxes and magnitudes of spectrophotometric
+standards.
+
+
+# Installation
+
+The `bbf` package works on `python>=3.9<3.13` for Linux and macos. It should
+work on Windows too, but it has not been tested.
+
+| :warning: `bbf` relies for the moment on a [modified version of `sncosmo`](https://github.com/nregnault/sncosmo) that must be installed separatly |
+|---|
+
+
+## Install using conda (recommended)
+
+```bash
+conda install -c conda-forge bbf
+pip install git+https://github.com/nregnault/sncosmo
+```
+
+
+## Install using pip
+
+* Installing `bbf` from `pip` requires to install
+  [SuiteSparse](http://www.suitesparse.com) which is not installable from `pip`.
+  On Debian/Ubuntu systems, the command `sudo apt install libsuitesparse-dev`
+  suffices. Or you can compile `SuiteSparse` from
+  [sources](https://github.com/DrTimothyAldenDavis/SuiteSparse). Or a simpler
+  alternative is to install `scikit-sparse` from `conda`:
+
+  ```bash
+  conda install -c conda-forge scikit-sparse
+  ```
+
+* `cmake` and a C++ compiler with `OpenMP` support are required. On Linux, `gcc`
+  supports `OpenMP` out of the box, and `cmake` is installed as needed during
+  `bbf` installation. On macos an extra installation is required:
+
+  ```bash
+  # for macos only
+  conda install cmake llvm-openmp
+  ```
+
+* `sncosmo` fork must be installed separatly with:
+
+  ```bash
+  pip install bbf git+https://github.com/nregnault/sncosmo
+  ```
+
+* Finally install `bbf`:
+
+  ```bash
+  pip install bbf
+  ```
+
+## Install from sources
+
+* If you prefer installing from sources, ensure **git lfs** is installed (have a
+  `git lfs`, if the command is missing install it with `conda install git-lfs;
+  git lfs install`).
+
+* Then follow the steps from the [Install using pip](#install using pip)
+  section, and replace the last step with:
+
+  ```bash
+  git clone clone git@gitlab.in2p3.fr:lemaitre/bbf.git
+  cd bbf
+  pip install -e .
+  ```
+
+* To run the tests suite, install the required dependencies, then run `pytest`:
+
+  ```bash
+  pip install -e .[test]
+  pytest
+  ```
+
+* If you are a developper and want to work on the `bbf` C/C++ extension,
+  insall the package with:
+
+  ```bash
+  pip install nanobind ninja scikit-build-core[pyproject]
+  VERBOSE=1 pip install --no-build-isolation -Ceditable.rebuild=true -ve .
+  ```
+
+## Installing the Lemaitre bandpasses
+
+If you plan to use the latest version of the megacam6*, *ztf* and *hsc*
+passbands, install the `lemaitre.bandpasses` package:
+
+```bash
+pip install lemaitre-bandpasses
+```
+
+or
+
+```bash
+git clone https://gitlab.in2p3.fr/lemaitre/lemaitre/bandpasses
+cd bandpasses
+git lfs pull
+pip install .
+```
+
+
+# Getting started
+
+The goal of `bbf` is to efficiently compute broadband fluxes and magnitudes,
+i.e. quantities of the form:
+
+$$f_{xys} = \int S(\lambda) \lambda T_{xys}(\lambda) d\lambda$$
+
+where $\lambda$ is the SED of an object, $T_{xyz}(\lambda)$ is the bandpass of
+the instrument used to observe it. $T$ may depend on the focal plane position of
+the object and, if the focal plane is a mosaic of sensors, on the specific
+sensor $s$ where the observation is made. In practice, $x,y$ are coordinates, in
+pixels, in the sensor frame, and $s$ is a unique sensor index (or amplifier
+index).
+
+Computing magnitudes requires an additional ingredient: the flux of a reference
+spectrum $S_{ref}(\lambda)$, usually the AB spectrum, integrated in the same
+passband (same sensor, same position).
+
+$$m = -2.5 \log_{10} \left(\frac{\int S(\lambda) \lambda T_{xyz}(\lambda) d\lambda}{\int S_{ref}(\lambda) \lambda T_{xyz}(\lambda) d\lambda}\right)$$
+
+To compute these integrales, `bbf` uses the technique implemented in `nacl`,
+which consists in projecting the bandpasses and SED on spline bases:
+
+$$S(\lambda) = \sum_i \theta_i {\cal B}_i(\lambda)$$
+
+and
+
+$$T(\lambda) = \sum_j t_j {\cal B}_j(\lambda)$$
+
+If we precompute the products $G_{ij} = \int \lambda {\cal B}_i(\lambda) {\cal B}_j(\lambda) d\lambda$
+the integrals above can be expressed as a simple contraction:
+
+$$f = \theta_i G_{ij} t_j$$
+
+where $G$ is very sparse, since the B-Splines ${\cal B}_i$ have a compact
+support. If the bandpass $T$ is spatially variable, the $t_j$ coefficients are
+themselves developped on a spatial spline basis.
+
+$$t_j = \sum_{kj} \tau_{kj} {\cal K}(x,y)$$
+
+The contraction above is then of the form: ...
+
+
+## FilterSets and StellarLibs
+
+`bbf` implements two main kind of objects: `FilterLib`, which holds a set of
+band passes, projected on spline bases (${\cal K_j(x,y)}$ and ${\cal
+B}_i_(\lambda)$), and `StellarLib` which manages a set of spectra, also
+projected on a spline basis (not necessily the splines used for the filters).
+
+
+## Loading a filter lib
+
+Building a complete version of a `FilterLib` requires some care. The standard
+`FilterLib` used in the Lemaître analysis is build and maintained within the
+package `lemaitre.bandpasses`. To access it:
+
+``` python
+from lemaitre import bandpasses
+
+flib = bandpasses.get_filterlib()
+```
+The first time this function is called, the `FilterLib`` is built and cached. The subsequent calls
+access the cached version, and never take more than a few milliseconds.
+
+
+## Loading Stellar Libraries
+
+As of today, `bbf` implements two kinds of StellarLibs: pickles and Calspec. An
+interface to gaiaXP is in development.
+
+To load the pickles library:
+
+``` python
+
+import bbf.stellarlib.pickles
+pickles = bbf.stellarlib.pickles.fetch()
+```
+
+To load the most recent version of Calspec:
+
+``` python
+import bbf.stellarlib.calspec
+calspec = bbf.stellarlib.calspec.fetch()
+```
+
+
+## Computing Broadband fluxes
+
+With a `FilterSet` and a `StellarLib` in hand, one can compute broadband fluxes
+and broadband mags.
+
+
+### Broadband fluxes
+
+``` python
+import bbf.stellarlib.pickles
+from lemaitre import bandpasses
+
+flib = bandpasses.get_filterlib()
+pickles = bbf.stellarlib.pickles.fetch()
+
+# number of measurements
+nmeas = 100_000
+
+# which stars ?
+star = np.random.choice(np.arange(0, len(pickles)), size=nmeas)
+
+# in which band ?
+band = np.random.choice(['ztf::g', 'ztf::r', 'ztf::I'], size=nmeas)
+
+# observation positions
+x = np.random.uniform(0., 3072., size=nmeas)
+y = np.random.uniform(0., 3080., size=nmeas)
+sensor_id = np.random.choice(np.arange(1, 65), size=nmeas)
+
+fluxes = flib.flux(pickles, star, band, x=x, y=y, sensor_id=sensor_id)
+```
+
+
+### Broadband magnitudes
+
+To convert broadband fluxes into broadband magnitudes, we need to compute the
+reference fluxes, in the same effective measurement band passes. This is done
+using an auxiliary object called `MagSys`:
+
+``` python
+
+from bbf.magsys import SpecMagSys
+import bbf.stellarlib.pickles
+from lemaitre import bandpasses
+
+flib = bandpasses.get_filterlib()
+pickles = bbf.stellarlib.pickles.fetch()
+
+# number of measurements
+nmeas = 100_000
+
+# which stars ?
+star = np.random.choice(np.arange(0, len(pickles)), size=nmeas)
+
+# in which band ?
+band = np.random.choice(['ztf::g', 'ztf::r', 'ztf::I'], size=nmeas)
+
+# observation positions
+x = np.random.uniform(0., 3072., size=nmeas)
+y = np.random.uniform(0., 3080., size=nmeas)
+sensor_id = np.random.choice(np.arange(1, 65), size=nmeas)
+
+ms = SpecMagSys('AB')
+mags = ms.mag(pickles, star, band, x=x, y=y, sensor_id=sensor_id)
+```
+
+
+# License
+
+`bbf` is distributed under the terms of the
+[MIT](https://spdx.org/licenses/MIT.html) license.