Pygfunction

New features

* [Issue 276](https://github.com/MassimoCimmino/pygfunction/issues/276) - Added functions to the `boreholes` module for the generation of rectangular fields in a staggered configuration.

Enhancements

* [Issue 291](https://github.com/MassimoCimmino/pygfunction/issues/291) - Simplified the expressions in heat_transfer._finite_line_source_steady_state`. The function is now approximately 25% faster.

Bug fixes

* [Issue 255](https://github.com/MassimoCimmino/pygfunction/issues/255) - Default to an `orientation` of `0.` when `tilt` is `0.` in `boreholes.Borehole` class.
* [Issue 266](https://github.com/MassimoCimmino/pygfunction/issues/266) - Fixed an issue were `SingleUTube.get_temperature` returned incorrect results when the fluid-to-pipe wall resistance was small in coaxial configurations. New coefficients are introduced in `SingleUTube.coefficients_temperature` and `SingleUTube.coefficients_outlet_fluid_temperature`. This also solves issues encountered when the fluid mass flow rate is small.
* [Issue 274](https://github.com/MassimoCimmino/pygfunction/issues/274) - Fixed scalar assignment from ndim-1 array. It is deprecated as of `numpy` version `1.25`. Only ndim-0 arrays can be treated as scalars.
* [Issue 285](https://github.com/MassimoCimmino/pygfunction/issues/285) - Use `numpy.complex128` instead of `numpy.cfloat`. This is to comply with backward-incompatible changes introduced in `numpy` version `2.0`.
* [Issue 286](https://github.com/MassimoCimmino/pygfunction/issues/286) - Fixed incorrect coefficients in `pipes.SingleUTube._continuity_condition_base` which caused errors in all dependent class methods when `segment_ratios` were not symmetric around the borehole mid-length.
* [Issue 298](https://github.com/MassimoCimmino/pygfunction/issues/298) - Fixed incorrect coefficients in `pipes._basePipe`, `pipes.MultipleUTube` and `pipes.IndependentMultipleUTube` which caused errors in fluid temperature profiles and outlet fluid temperatures.

Enhancements

* [Issue 204](https://github.com/MassimoCimmino/pygfunction/issues/204) - Added support for Python 3.9 and 3.10. [CoolProp](https://www.coolprop.org/) is removed from the dependencies and replace with [SecondaryCoolantProps](https://github.com/mitchute/SecondaryCoolantProps).

Bug fixes

* [Issue 231](https://github.com/MassimoCimmino/pygfunction/issues/231) - Fixed an issue where the evaluation of g-functions at very low times raises an error due a singular matrix. g-Functions below a threshold time value `t=max(r_b)**2/(25*alpha)` are now linearized.

Other changes

* [Issue 229](https://github.com/MassimoCimmino/pygfunction/issues/229), [Issue 247](https://github.com/MassimoCimmino/pygfunction/issues/247) - Added citation to IGSHPA conference paper on *pygfunction* v2.2 in the documention. Added a `CITATION.cff` file to suggest a correct citation on github.
* [Issue 230](https://github.com/MassimoCimmino/pygfunction/issues/230) - Configured github actions to publish *pygfunction* on Pypi on creation of a release on github.

Bug fixes

* [Issue 220](https://github.com/MassimoCimmino/pygfunction/issues/220) - Fixed the expected line length in `boreholes.field_from_file()` to correctly import fields of inclined boreholes.
* [Issue 224](https://github.com/MassimoCimmino/pygfunction/issues/224) - Fixed an issue where tests were not run on maintenance branches.

New features

* [Issue 50](https://github.com/MassimoCimmino/pygfunction/issues/50) - Implemented inclined boreholes for the evaluation of *g*-functions. The implementation includes an approximation of the FLS solution for inclined boreholes based on the method of Cimmino (2021) (see [Issue 138](https://github.com/MassimoCimmino/pygfunction/issues/138)). The `'equivalent'` solver is not yet supported.
* [Issue 138](https://github.com/MassimoCimmino/pygfunction/issues/138) - Implemented the approximation of the finite line source solution of Cimmino (2021). The approximation avoids the numerical evaluation of integrals. This speeds up the calculation of g-functions when enabled.
* [Issue 148](https://github.com/MassimoCimmino/pygfunction/issues/148) - Implemented `effective_borehole_thermal_resistance()` and `local_borehole_thermal_resistance()` methods for all pipe classes. Deprecated `pipes.borehole_thermal_resistance()`, which computed the effective borehole thermal resistance. It will be removed in `v3.0.0`. Implemented a new `update_thermal_resistances()` method to all pipe classes. This method allows to update the delta-circuit of thermal resistance of the boreholes based on provided values for the fluid thermal resistances. This allows simulations with time-variable fluid thermal resistances.

Enhancements

* [Issue 152](https://github.com/MassimoCimmino/pygfunction/issues/152) - Vectorized `coefficients_temperature` and `_general_solution` in `pipe` objects to accept depths `z` as an array. This speeds up calculations for `get_temperature` and `get_borehole_heat_extraction_rate` class methods.
* [Issue 183](https://github.com/MassimoCimmino/pygfunction/issues/183) - Vectorized `pipes.multipole()` and `pipes._Fmk()` to decrease the calculation time of `pipes.thermal_resistances()`. A `memoization` technique is implemented to reduce computation time for repeated function calls to further speed-up the initialization of `Pipe` and `Network` objects.
* [Issue 198](https://github.com/MassimoCimmino/pygfunction/issues/198) - Refactored the `'detailed'` solver to evaluate same-borehole thermal response factors in a single call to `finite_line_source_vectorized()`. This speeds up calculations of *g*-functions using the `'detailed'` solver.
* [Issue 199](https://github.com/MassimoCimmino/pygfunction/issues/199) - Changed the integral bounds to avoid repeated evaluation of integrals over semi-infinite intervals. This speeds up calculations of *g*-functions using all solvers and the evaluation of the finite line source solution with `time` as an array.
* [Issue 206](https://github.com/MassimoCimmino/pygfunction/issues/206) - Refactored `boreholes.find_duplicates()` to use `scipy.spatial.distance.pdist()` for the calculation of distances between boreholes. This leads to faster initialization of the `gFunction` class for large borefields.

Other changes

* [Issue 80](https://github.com/MassimoCimmino/pygfunction/issues/80) - Added references to the `pipes` module for the evaluation of borehole thermal resistances.
* [Issue 171](https://github.com/MassimoCimmino/pygfunction/issues/171) - Refactored modules and examples to use the built-in `enumerate(x)` instead of `range(len(x))`.
* [Issue 172](https://github.com/MassimoCimmino/pygfunction/issues/172) - Refactored reports of calculation time to use `time.perf_counter()` instead of `time.time()`.
* [Issue 173](https://github.com/MassimoCimmino/pygfunction/issues/173) - Refactored strings into f-strings instead of using `str.format()`.
* [Issue 177](https://github.com/MassimoCimmino/pygfunction/issues/177) - Converted `setup.py` script to `setup.cfg` and `pyproject.toml` files. This is motivated by [PEP518](https://www.python.org/dev/peps/pep-0518/) and [PEP621](https://www.python.org/dev/peps/pep-0621/).
* [Issue 179](https://github.com/MassimoCimmino/pygfunction/issues/179) - Refactored tests to use the `pytest` package instead of `unittests`.
* [Issue 180](https://github.com/MassimoCimmino/pygfunction/issues/180) - Configured `tox` and github actions for continuous integration.

Bug fixes

* [Issue 192](https://github.com/MassimoCimmino/pygfunction/issues/192) - Fixed comparison of `time` with `numpy.inf` in `heat_transfer.finite_line_source` that caused the function to fail when `time` is an array.
* [Issue 193](https://github.com/MassimoCimmino/pygfunction/issues/193) - Fixed `heat_transfer._finite_line_source_integrand`, `heat_transfer._finite_line_source_equivalent_boreholes_integrand`, and `heat_transfer._finite_line_source_steady_state` to return an array of zeros of the expected shape when `reaSource==False and imgSource==False`.
* [Issue 196](https://github.com/MassimoCimmino/pygfunction/issues/196) - Fixed "invalid escape sequence" warnings when running tests on github actions.
* [Issue 202](https://github.com/MassimoCimmino/pygfunction/issues/202) - Added missing package `recommonmark` to requirements for documentation and development.
* [Issue 208](https://github.com/MassimoCimmino/pygfunction/issues/208) - Fixed an issue where `boreholes.field_from_file()` failed when the text file only contained 1 borehole.

New features

* [Issue 36](https://github.com/MassimoCimmino/pygfunction/issues/36) - Added a `Coaxial` class to the `pipes` module to model boreholes with coaxial pipes.
* [Issue 135](https://github.com/MassimoCimmino/pygfunction/issues/135) - Added functionality for non-uniform discretization of the segments along the boreholes. This increases the accuracy of *g*-function calculations for the same number of segments when compared to a uniform discretization. Segment lengths are defined using the `segment_ratios` option in the `gFunction` class. A `discretize` function is added to the `utilities` module to generate borehole discretizations using an expanding mesh.
* [Issue 146](https://github.com/MassimoCimmino/pygfunction/issues/146) - Added new solver `'equivalent'` to the `gFunction` class. This solver uses hierarchical agglomerative clustering to identify groups of boreholes that are expected to have similar borehole wall temperatures and heat extraction rates. Each group of boreholes is represented by a single equivalent borehole. The FLS solution is adapted to evaluate thermal interactions between groups of boreholes. This greatly reduces the number of evaluations of the FLS solution and the size of the system of equations to evaluate the g-function.

Enhancements

* [Issue 118](https://github.com/MassimoCimmino/pygfunction/issues/118) - Refactored checks for stored `_BasePipe` and `Network` coefficicients to use `numpy.all()`. This decreases calculation time.
* [Issue 119](https://github.com/MassimoCimmino/pygfunction/issues/119) - Refactored `Network` class to change how coefficient matrices are calculated. This decreases calculation time.
* [Issue 132](https://github.com/MassimoCimmino/pygfunction/issues/132) - Refactored `SingleUtube` and `MultipleUTube` classes to eliminate `for` loops in the calculation of matrix coefficients. This decreases calculation time when `nSegments>>1`.
* [Issue 133](https://github.com/MassimoCimmino/pygfunction/issues/133) - The `nSegments` argument is now able to take in the number of segments for each borehole as a list. Each borehole must be split into at least 1 segment, and the length of the segment list must be equal to the number of boreholes.
* [Issue 141](https://github.com/MassimoCimmino/pygfunction/issues/141) - Changed the calculation of the convective heat transfer coefficient in the transition region (`2300. < Re < 4000.`) by `convective_heat_transfer_coefficient_circular_pipe()`. The Nusselt number is now interpolated between the laminar value (at `Re = 2300.`) and the turbulent value (at `Re = 4000.`). This avoids any discontinuities in the values of the convective heat transfer coefficient near `Re = 2300.`.

Other changes

* [Issue 93](https://github.com/MassimoCimmino/pygfunction/issues/93) - Reformatted `pipes` and `networks` modules to use the `` matrix product operator introduced in [PEP465](https://www.python.org/dev/peps/pep-0465/). This improves readability of the code.
* [Issue 100](https://github.com/MassimoCimmino/pygfunction/issues/100) - Replaced calls to `numpy.asscalar()` with calls to `array.item()`. `numpy.asscalar()` is deprecated as of `numpy` version `1.16`.
* [Issue 124](https://github.com/MassimoCimmino/pygfunction/issues/124) - Reformatted `pipes`and `networks` modules to clarify the expected values for `m_flow` parameters. These are replaced by any of `m_flow_pipe`, `m_flow_borehole` or `m_flow_network` depending on the function or class method. Added a nomenclature of commonly used variables to the documentation.
* [Issue 125](https://github.com/MassimoCimmino/pygfunction/issues/125) - Refactored class methods and docstrings in `Pipe` and `Network` objects to better represent the expected shapes of array inputs and outputs.
* [Issue 139](https://github.com/MassimoCimmino/pygfunction/issues/139) - Updated requirements for numpy from version `1.19.2` to `1.20.1`. Clarified the Python version `3.7` requirement in the `README.md` file.
* [Issue 154](https://github.com/MassimoCimmino/pygfunction/issues/154) - Replaced `numpy.int` and `numpy.bool` dtypes in array initializations with built-in types `int` and `bool`. `numpy.int` and `numpy.bool` are deprecated as of `numpy` version `1.20`.
* [Issue 158](https://github.com/MassimoCimmino/pygfunction/issues/158) - Changed default parameter values for *g*-function calculations. The `gFunction` class now uses the `'equivalent'` solver by default and a non-uniform discretization of `nSegments=8` given by `utilities.segment_ratios()`.
* [Issue 160](https://github.com/MassimoCimmino/pygfunction/issues/160) - Deprecated functions `gfunction.uniform_heat_extraction`, `gfunction.uniform_temperature`, `gfunction.equal_inlet_temperature` and `gfunction.mixed_inlet_temperature`. They will be removed in `v3.0.0`.

Bug fixes

* [Issue 99](https://github.com/MassimoCimmino/pygfunction/issues/99) - Fixed an issue where `MultipleUTube._continuity_condition()` and `MultipleUTube._general_solution()` returned complex valued coefficient matrices.
* [Issue 130](https://github.com/MassimoCimmino/pygfunction/issues/130) - Fix incorrect initialization of variables `_mix_out` and `_mixing_m_flow` in `Network`.
* [Issue 155](https://github.com/MassimoCimmino/pygfunction/issues/155) - Fix incorrect initialization of variables in `Network` and `_BasePipe`. Stored variables are now initialized as `numpy.nan` instead of `numpy.empty`.
* [Issue 159](https://github.com/MassimoCimmino/pygfunction/issues/159) - Fix `segment_ratios` function in the `utilities` module to always expect 0 < `end_length_ratio` < 0.5, and allows for `nSegments=1` or `nSegments=2`. If 1<=`nSegments`<3 then the user is warned that the `end_length_ratio` parameter is being over-ridden.