Pyfstat

- Pinned to `numpy<1.24.0` to avoid incompatibility with `ptemcee`.

- This is the first PyFstat release to officially support python 3.11.
- LALSuite is introducing an SFT specification and filename update
- see https://dcc.ligo.org/T040164-v2/public)
- This version of PyFstat is pinned to `lalsuite<=7.11` (or `lalpulsar<6.0`)
so that it is ensured to keep working with the old convention.
- Next PyFstat release will adapt to the LALSuite changes.
- Added `get_official_sft_filename()` utility function to ease migration.
- Improvements to `injection_parameters` module with new priors logic
(see documentation);
old input style still supported for now but deprecated.
- `Writer`: improved timestamps handling:
support 1-column format (without nanoseconds),
which has been the LALPulsar default for a while.
- Changed `ComputeFstat.write_atoms_to_file()` method
to use consistent `%%` comment markers.
- Fixed segfault in `get_semicoherent_single_IFO_twoFs()` with recent LALSuite
(need to properly copy FstatAtomVector struct).
- Fixed `TransientGridSearch` when not setting any actual transient parameters.
- Added (h0,cosi)<->(aplus,across) functions to `utils.converting`.
- Added `utils.atom` submodule with tools related to F-stat atoms.
- `utils.get_sft_as_arrays()` now user-accessible
- `Writer`: warning about inferring parameters (in `noiseSFTs is not None` case)
downgraded to info message
- improvements to documentation and test suite

- fixed finalizer setup for calling `ComputeFstat` and its children
in context-manager mode
- reverted "walrus operators" (`:=`) and use of `Literal` typing checks
to facilitate `python 3.7` backwards compatibility
(not officially supported from release, but can be easily restored on branches / local clones)
- lalsuite-from-source install instructions no longer included in README, now live on wiki
- fixed logging use in examples
- improved testing of tutorial notebooks

- refurbished logging system:
- on `import.pyfstat`, stdout logging at INFO level is activated
unless there are already handlers attached to the root logger
- recommended to further call `pyfstat.set_up_logger` and define an output log file,
as demonstrated in our examples
- see https://pyfstat.readthedocs.io/en/v1.18.0/pyfstat.html#module-pyfstat.logging for details
- removed the last global argparse options `--quite` and `--verbose`,
along with the remainders of the `helper_functions.set_up_command_line_arguments()` function.
Please use `pyfstat.set_up_logger` instead to determine verbosity level.
- tests now by default print all >=WARNING messages even for passing cases
and full >=INFO for failing cases
- improved handling of LALSuite executables through `run_commandline`
- better stderr/stdout capture
- return is now either a `subprocess.CompletedProcess` object
or `None`
- default is now `return_output=False`
- `log_level` argument removed
(please use `pyfstat.set_up_logger` instead)
- capture and handling of output from SWIG-wrapped LALSuite functions
likely to be further improved in future versions
- refactored `helper_functions` module into `utils` subpackage
with multiple source files;
- user can access all functions directly as `utils.some_function`
without worrying about the level one further down
- moved `matplotlib` setup into new `utils.safe_X_less_plt()`
- removed deprecated/unused helper functions
- `get_peak_values`
- `get_comb_values`
- `get_sft_array`
- can install with `NO_LALSUITE_FROM_PYPI` environment variable,
e.g. to avoid duplication of dependencies from conda and pip
(now used this way in recommended `pyfstat-dev.yml`)
- removed `peakutils` dependency
- optional `[dev]` set of dependencies now also includes `docs` dependencies
- added `sphinx_autodoc_typehints` to `docs` dependencies
and updated pinned versions of other sphinx packages
- `DetectorStates`: fixed passing plain lists as values of a `timestamps` dict

- dropped python 3.7 support
- dropped dependency on `lalapps` and now requiring `lalpulsar>=5.0.0` instead,
where LALSuite executables now live
(corresponding to `lalsuite>=7.7`)
- there is a `get_lal_exec()` helper function to still allow running
on old installations where the executables live in `lalapps`
- removed most of the old package-level hardcoded `argparse` options,
this should reduce conflicts when users import it in their own caller scripts:
- `--clean` to be given as an argument to supporting classes
- `-N` to be given as class argument `num_threads`
to the one class `FrequencyModulatedArtifactWriter` that supported it
- `--setup-only` and `--no-template-counting` to be given as class arguments
to the (now deprecated) `MCMCFollowUpSearch`
- `--no-interactive` was not supported anywhere
- LaTeX no longer enabled for plotting by default
- removed `bashplotlib` dependency and SFT timestamps ASCII art
- removed fallbacks in case `tqdm` is not available,
which is a dependency anyway
- `snr` class: fixed behaviour when instantiating with a dictionary of timestamps
- removed old backwards compatibility code from `FrequencyModulatedArtifactWriter`
- developers: updated pre-commit hooks

- include local versions of autocorr functions from `ptemcee`
to restore compatibility with `numpy>=1.23.0`
- `Writer`: remove deprecated `timestampsFiles` option,
please use the more general `timestamps` instead
- added `BtSG` option to transient searches
(transient Bayes factor from PGM2011)
- `pyTransientFstatMap` is now available via `import pyfstat`
- some refactoring of internal detection statistics functions
- use of `lalapps_tconvert` replaced by new `gps_to_datestr_utc()` helper function
(which uses `XLALGPSToUTC` and `datetime`)
- fix CUDA context detaching at garbage collection time for
`ComputeFstat` and `TransientGridSearch` classes
- using `weakref`
- should not require any caller code changes in standard use cases
- but if user wants to initiate more than one such object from one session/script,
these should be used in context manager style (`with ComputeFstat as` etc)
- remove redundant complex entries from output of `tcw_fstat_map_funcs.reshape_FstatAtomsVector()`
- streamline installation instructions for developers
and remove single-use helper bash scripts