Dust model (3D) with multiple layers d12

[zonca]

• set lmax of smoothing to 3*nside-1
• support for output units
• Imported InterpolatingComponent from so_pysm_models
• implementation of bandpass integration and debug MPI
• update the test suite to match the new API
• support for MapDistribution in InterpolatingComponent
• added mpi examples
• test extragalactic
• trapz for dust
• bandpass integration for InterpolatingComponent
• trapz for spdust
• trapz step inplace jitted funciton
• trapz for power law
• [bugfix] fixed error trapz for unique frequency
• export check_freq_input
• implemented bandpass integration in InterpolatingComponent
• removed placeholder apply_bandpass function
• there are no weights for nside 16 and lower
• attach unit to output if input has a unit
• do not set iter=1
• bugfix in interface
• fixed conflicts
• example run at 4096
• moved mpi_smoothing into mpi.py
• simple CMBMap model and unit test
• ignore .out .log
• job script for popeye
• add memreport
• [bugfix] fix imports in mpi.py
• [bugfix] wrong variable name
• 10 nodes run
• implement trapz in a1 model
• [bugfix] map_dist was not passed along
• weighting in Jy/sr
• simplify test, we are now doing weighting in Jy/sr
• use rotator instead of coord argument
• fixed mpi smoothing
• import mpi smoothing
• weighted average for unit conversion
• moved check_freq_input to utils
• improve docstring of apply smoothing and coord conversion
• implement bandpass unit conversion
• use check_freq_input in bandpass unit conversiona
• fix bandpass unit conversion for single frequency
• link to tutorial
• recognize if we have a identity rotator
• disable debugging print
• new version of astropy gives a slightly different result
• fix typo and run black
• Cache maps in interpolator
• Explain how to clear the cache
• add CMB model c2 from template
• add numba and h5py to requirements for readthedocs
• support both separate and single map in CMBMap
• implementation of lensed CMB model c1
• suppress exception about not providing any input map
• integrate 10 points in bandpass
• allocate MPI shared buffer
• 1 node test to write/read from shared memory
• communication with node communicator on multiple nodes
• completed implementation, slicing local pixels
• remove unused import
• black formatting
• suppress warnings on rank > 0
• remove printing and barrier
• improve read mpi test also check arrays
• simplify MPI, use automatic ranking, add barrier
• use 4096 input maps
• move mpi4py import inside function
• set version to 3.1.dev
• explicitely free the shared memory buffer
• also call the garbage collector
• create fake timelines in MPI example
• imported docs from PySM 2
• link new pages to index
• reconfigure environment for RTD
• moved docs from introduction to index
• removed outdated docs on how to use
• work in progress notice on models
• notebook based tutorial docs
• print doc
• add ipykernel and pandoc on readthedocs
• add pip ad dependency
• switch to version 2 specify python and astropy version
• install the package
• specify kernel name
• point to docs
• mpi docs
• update requirements
• install ipykernel and nbsphinx on Travis
• remove hidden metadata from cell
• remove docs build on travis
• link to notebook tutorials
• mention MPI requirements
• Create LICENSE
• modify name for PyPI
• do not update astropy_helpers at install time (for conda-forge)
• add LICENSE to PyPI package
• tag 3.1.0
• switch version to dev
• Revert "do not update astropy_helpers at install time (for conda-forge)"
• support scalar dust temperature
• implementation of d0 and test
• implementation of d2 and test
• implementation of d3 and test
• build on RTD with Python 3.6
• added documentation for d0
• implement s0 and test
• implement s2 and test
• implemented s3 curved synchrotron
• use sphinx math dollar
• mention PySM 2 paper in summary in homepage
• removed empty files
• removed docstrings from all the get_emission methods
• added get_emission method to base class with docstring
• add conda and pip to installation docs
• Added HD17 model
• Added docs to HD17 method.
• Removed debug print statement
• Reordered shape of get_emission output to (nfreq, npol, npix)
• Ammended for new API calling one channel at a time.
• Refactored get_emission to calculate each frequency individually and accumulate for bandpass average.
• Added some comments
• switch readthedocs to pip
• use newer numpy on travis
• docs: installation instructions in readme and docs
• Add missing requirements (healpy, numba and toml)
• fix d6 model initialization
• fix computation of d6 emission
• add unit test
• fix: always convert input freq to GHz
• fix: run utils.check_input_freq also in interpolating
• feat: return plain np.array from check_freq
• feat: add HD2017 model definition as d7
• test: unit test for HD2017
• fix: remove unused arguments and black formatting
• set version to 3.1.1
• set version to 3.1.dev
• rebuild on latest astropy package template
• update also travis configuration
• set version to 3.1.2
• removed entry_points and requirements.txt
• remove entry-points
• fix: all flake8 style issues
• fix: line length issue
• style: suppress import * warnings
• test: remove tests on windows
• docs: requirements for building docs
• add pandoc to travis
• test: do not test astropy 3.x, too old
• docs: don't fail on warning
• docs: removed templates
• docs: fix link formatting
• test: add Pygments as requirements
• write requirements in README
• Added CHANGES.rst file
• add info about tox
• docs: add executed notebooks for readthedocs
• change package name to pysm3
• back to development
• Added nside overide for template component class
• Added docstring to new read_map nside kwarg
• Added nside_uval arg for hd17 model
• Added docstring for nside_uval arg
• expand docstring for Sky
• fix: units and trailing whitespace
• fix: pep8
• fix: package naming in docs
• docs: add info about PR 37
• PyPI and Conda badges and Astropy
• Update README.rst
• feat: moved hd2017 to its own module
• feat: implementation of the HD2017-based d5 model
• feat: implementation of d8, added uval argument
• feat: explain default for uval in docstring
• feat: implement check local folder first
• use importlib.pkg_resources to load presets.cfg
• fix: add extra requirement for python < 3.7
• docs: updated changelog
• fix: use consistent naming
• docs: add docs for input templates
• docs: link to release guide
• updated CHANGES and change version to 3.2.0
• style: ran black on setup.py
• docs: install at NERSC
• fix url for PyPI
• docs: consolidate installation instructions into docs
• back to development: 3.2.1.dev
• docs: docstring for normalize_units
• fix: update run mpi tests to new setup
• ci: run MPI tests on Travis-CI
• ci: run MPI tests with the env configured by tox
• test: add mpi4py as extra requirement for tests
• ci: run mpi tests only with one tox env
• renamed package to pysm3 and use poetry
• poetry.lock with base test environment
• support multiple numpy versions
• increase version to 3.3.0
• test: do not use poetry in tox
• ci: configure readthedocs for poetry
• update poetry.lock
• update poetry.lock
• package: fix extras
• test: add back setup.cfg for coverage and pytest
• ci: fix folder on Travis
• project details for PyPI
• doc: update CHANGES.rst
• use instead version 3.2.1
• update docs
• filter warnings and pysm3
• doc: update notebooks
• doc: mention renamed package in CHANGES
• doc: removed the example notebook in the repo root
• set date of release
• bump version to 3.2.2
• feat: get version from the package, remove astropy_init
• add dev to version
• feat: print warning and return zero for CIB outside of range
• pkg: add importlib resources for Python 3.6
• ready to release 3.2.2
• feat: set verbose=False to map2alm
• changed bandpass_unit_conversion and add unit test
• feat: use float64 keys for frequency in cached maps dict
• fix: interpolator with no pol was returning IQU
• Revert "fix: interpolator with no pol was returning IQU"
• feat: remove has_polarization for interpolating
• removed from astropy
• feat: handle weights None (tophat)
• tests: import unit conversion unit tests from PySM 2
• feat: support input unit in bandpass_unit_conversion
• feat: allow default weights to None
• fix: normalize weights
• test: compare with planck
• feat: read RIMO from NERSC
• feat: filter out gains too low
• feat: expose cut to API
• fix: codestyle errors
• test: compare with PySM 2
• compare with tod2flux
• compare with tod2flux removing the \nu^-1 IRAS factor
• use utils.bandpass_unit_conversion in CMB
• disable normalization of weights when converting to other units
• fix single frequency conversion
• note about -2 spectral index in dust
• fix: disable weights normalization for CMB
• fix: enabled again normalization to RJ and added docs
• fix: don't use 2: slicing
• packaging: more flexible requirement on numba
• ci: point badge to travis-ci.com
• fix: support scalar freq and mbb_index
• docs: add docs about bandpass integration
• docs: minor improvements, typos
• fix: fix mpi example
• packaging: add requirement on importlib-metadata
• set version to 3.3.0
• removed testing with numpy 1.16
• updated changelog
• point to travis-ci.com
• increase timeout for getting data to 90s
• added documentation for the dust models d7 and d8
• Reproduce PySM 2 templates for Dust (Reproduce PySM 2 templates for Dust galsci/pysm#66)
• disable development version of numpy because it doesn't build on Travis
• remove tags
• Reproduce PySM 2 Synchrotron model s1 (Reproduce PySM 2 Synchrotron model s1 galsci/pysm#71)
• Mention numba threading in docs
• files internal to the package
• imported license from Astropy package template
• import new Astropy package template, remove poetry
• fix requirements
• update Sphinx conf.py
• remove windows
• remove mac os
• add Ubuntu packages
• run MPI test
• remove Travis CI
• remove poetry lock file
• use the tox python
• typo in readthedocs config
• remove docs about poetry
• doc: remove link in docstring
• Github actions status badge
• rename master to main in all docs
• Updated changelog
• docs: fix README typo
• remove mention of poetry in README
• doc: release instructions in README.rst
• remove old license
• authors and start of bibliography
• first full draft
• build paper
• how to cite
• use comma instead of braces
• minor fixes
• give name to paper workflow
• fix citations
• setup linkcheck to run weekly
• Added affiliation and ORCID
• Small language changes
• Nicoletta's affiliation
• fix affiliations
• simplify acknowledgements by @jdborrill
• Standardize grammar structure in bullet point
• Moved repository under galsci Github organization
• Acknowledge computing
• remove weekly linkcheck
• info about support in the README
• contributing guidelines
• change titles
• fix typo in readme
• specify requirements in docs
• link changelog
• fix typo in development installation docs
• added statement of need to paper
• Apply suggestions from code review
• Update paper/paper.md
• replace in the microwave with in the microwave portion of the spectrum
• final spellcheck
• move license to root of repo
• add JOSS badge
• get also tex files in github action
• fix typo in JOSS badge
• Create CITATION
• Reference papers
• Update citation year in README
• feat: implemented dust layers model, test trivial case