Update bench branch

.github/workflows/build.yaml

@@ -0,0 +1,85 @@
+name: build_and_test
+
+on:
+  push:
+    branches:
+      - main
+      - lsst-dev
+      - master
+  pull_request:
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: 'latest'
+          environment-name: test
+          create-args: >-
+            python=3.11
+          channels: conda-forge,defaults
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install system dependencies
+        shell: micromamba-shell {0}
+        run: |
+          micromamba install -y astrometry rubin-libradtran -c conda-forge
+
+      - name: Install Spectractor with dependencies
+        shell: micromamba-shell {0}
+        run: |
+          pip install -v -e ".[dev]"
+          pip install git+https://github.com/LSSTDESC/getObsAtmo.git@main
+
+
+      - name: Download test data
+        shell: micromamba-shell {0}
+        run: |
+          wget -r -q -nc http://data.astrometry.net/5000/index-5002-24.fits
+          wget -r -q -nc http://data.astrometry.net/5000/index-5000-40.fits
+          mkdir -p $MAMBA_ROOT_PREFIX/envs/test/data/
+          mv data.astrometry.net/5000/index-*.fits $MAMBA_ROOT_PREFIX/envs/test/data/
+          export ASTROMETRYNET_DIR=$MAMBA_ROOT_PREFIX/envs/test
+
+      - name: List installed packages
+        shell: micromamba-shell {0}
+        run: |
+          micromamba list
+          pip list -v
+
+      - name: Run full chain test
+        shell: micromamba-shell {0}
+        run: |
+          pytest tests/test_fullchain.py --log-cli-level=INFO -v -rs --cov --cov-report lcov
+
+      - name: Run pytests
+        shell: micromamba-shell {0}
+        run: |
+          pytest tests/test_extractor.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+          pytest tests/test_simulator.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+          pytest tests/test_utils.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+          pytest tests/test_fitter.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+          pytest tests/test_multispectra.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+
+      - name: Run doctests and coverage
+        shell: micromamba-shell {0}
+        run: |
+          pytest spectractor \
+            --ignore=spectractor/astrometry.py \
+            --ignore=spectractor/parameters.py \
+            --ignore=spectractor/fit/mcmc.py \
+            -v --cov --cov-append --cov-report lcov \
+            --doctest-modules \
+            --doctest-continue-on-failure
+        continue-on-error: true
+
+      - name: Coveralls
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: coverage.lcov

coverage_and_test.sh → .github/workflows/coverage_and_test.sh

@@ -8,24 +8,24 @@ ls tests/data/*.fits
 for i in spectractor/*.py
 do
     echo Testing $i...
-    coverage run -a --source=spectractor $i
+    coverage run -m pytest -a --source=spectractor $i
 done
 
 for i in spectractor/extractor/*.py
 do
     echo Testing $i...
-    coverage run -a --source=spectractor $i
+    coverage run -m pytest -a --source=spectractor $i
 done
 
 for i in spectractor/simulation/*.py
 do
     echo Testing $i...
-    coverage run -a --source=spectractor $i
+    coverage run -m pytest -a --source=spectractor $i
 done
 
 for i in spectractor/fit/*.py
 do
     echo Testing $i...
-    coverage run -a --source=spectractor $i
+    coverage run -m pytest -a --source=spectractor $i
 done
 

.gitignore

@@ -17,9 +17,27 @@ Spectractor.egg-info/
 build/
 dist/
 *libradtran/
-outputs/
 docs/_build
 *_wcs/
 *.bak
 *.backup
 *.h5
+spectractor/version.py
+.sconsign.dblite
+config.log
+tests/.tests/
+*__pycache__/
+*.pickle
+*.cache/*
+*.json
+*.txt
+*.ipynb
+*.csv
+*.ecsv
+*.list
+*.dat
+*lcov
+*bak*
+*backup*
+notebooks/*
+tests/data/*

.readthedocs.yml

@@ -1,8 +1,31 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
 python:
-  version: 3.7
-  install:
-     - requirements: docs/requirements.txt
-     - method: pip
-       path: .
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .

README.md

@@ -1,6 +1,7 @@
 [![Build Status](https://travis-ci.org/LSSTDESC/Spectractor.svg?branch=master)](https://travis-ci.org/LSSTDESC/Spectractor)
 [![Coverage Status](https://coveralls.io/repos/github/LSSTDESC/Spectractor/badge.svg?branch=master)](https://coveralls.io/github/LSSTDESC/Spectractor?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/spectractor/badge/?version=latest)](https://spectractor.readthedocs.io/en/latest/?badge=latest)
+<a href="https://ascl.net/2104.004"><img src="https://img.shields.io/badge/ascl-2104.004-blue.svg?colorB=262255" alt="ascl:2104.004" /></a>
 
 # Spectractor
 
@@ -17,21 +18,34 @@ Some submodules complete the structures with generic functions:
 - `spectractor.logbook`: tools to read logbook `.csv` text files and get some metadata relative to the data images that are not contained in the header;
 - `spectractor.tools`: contains generic functions shared by all  the subpackages (fitting procedures, plotting functions, etc).
 
-
 ## Installation
 
-Spectractor is written in Python 3.7. The dependencies are listed in the `requirements.txt` file. To install Spectractor, just run
+Spectractor is written in Python 3.9. The mandatory dependencies are listed in the `requirements.txt` file. To install Spectractor, just run
 ```
 pip install -r requirements.txt .
 ```
-Be careful, Spectractor can perform fits using the MCMC library [emcee](https://emcee.readthedocs.io/en/stable/) with [mpi4py](https://mpi4py.readthedocs.io/en/stable/) and [h5py](https://www.h5py.org/).  The latter might be better installed using `conda install ...` command to get their own dependencies (openmp and hdf5).
 
-For the simulation of spectra, Spectractor needs the following external libraries:
-- [libradtran](http://www.libradtran.org/doku.php) to simulate atmospheric transmission: it needs the installation of [netcdf](https://www.unidata.ucar.edu/software/netcdf/) and a python 2 environment (for the compilation only, not the usage); `uvpsec` executable must in the user `$PATH` or the user has to set an environmental variable `$LIBRADTRAN_DIR` pointing to the install directory.
-- [pysynphot](https://pysynphot.readthedocs.io/en/latest/) to get the CALSPEC star spectra: the HST CALSPEC calibration spectra must be downloaded and the environment variable `$PYSYN_CDBS` must be created.
-- [astrometry.net](https://astrometrynet.readthedocs.io/en/latest/) (optional): needed to create World Coordinate System files from the images; `solve-field` executable must in the user `$PATH` or the user has to set an environmental variable `$ASTROMETRYNET_DIR` pointing to the install directory. Version below or equal v0.78 should be used.
+To simulate atmospheric transmission, Spectractor needs [libradtran](http://www.libradtran.org/doku.php) (optional). There are two ways to install this software:
+- use the [Rubin observatory conda package](https://anaconda.org/conda-forge/rubin-libradtran)
+```
+conda install -c conda-forge rubin-libradtran
+```
+- compile it from [sources](http://www.libradtran.org/doku.php): it needs the installation of [netcdf](https://www.unidata.ucar.edu/software/netcdf/) and a python 2 environment (for the compilation only, not the usage); `uvpsec` executable must in the user `$PATH` or the user has to set an environmental variable `$LIBRADTRAN_DIR` pointing to the install directory.
+
+To find accurate star centroids using astrometry, one can install [astrometry.net](https://astrometrynet.readthedocs.io/en/latest/) (optional). There are two ways to install this software:
+- use the anaconda package
+```
+conda install -c conda-forge astrometry
+```
+and then download and move [index files](http://astrometry.net/doc/readme.html#getting-index-files) in the `$CONDA_PREFIX/data` folder.
+- compile it from [sources](https://astrometrynet.readthedocs.io/en/latest/): it needs the installation of [netpbm](https://netpbm.sourceforge.net/) and [wcslib](https://www.atnf.csiro.au/people/mcalabre/WCS/wcslib/); `solve-field` executable must in the user `$PATH` or the user has to set an environmental variable `$ASTROMETRYNET_DIR` pointing to the install directory.
+
+For faster matrix multiplications, if available for a given computer configuration, one can install [sparse_dot_mkl](https://anaconda.org/conda-forge/sparse_dot_mkl):
+```
+conda install -c conda-forge sparse_dot_mkl
+```
 
-Detailled command lines for the installation of Spectractor and the external dependencies can be found in the file `.travis.yml`.
+Spectractor is able to perform parameter fits using the MCMC library [emcee](https://emcee.readthedocs.io/en/stable/) (optional) with [mpi4py](https://mpi4py.readthedocs.io/en/stable/) and [h5py](https://www.h5py.org/).  The latter might be better installed using `conda install ...` command to get their own dependencies (openmp and hdf5).
 
 ## Basic extraction
 
@@ -80,19 +94,3 @@ This object is also returned by the `Spectractor` function.
 
 A tutorial Jupyter notebook is available in the `notebooks` folder.
 
-## Detailed description
-
-### Dispersers
-
-### Shot noise
-
-### Rotation
-
-### Background extraction
-
-### Wavelength calibration
-#### First geometrical calibration
-#### Second calibration with line detection
-
-### Second order subtraction
-