v2023.12.0

What's Changed

• New kinetic models, bug fixes and refactoring by @gbouvignies in #176
• Update website to Docusaurus 3.0 by @gbouvignies in #178
• Bump actions/setup-node from 3 to 4 by @dependabot in #179
• Bump actions/checkout from 3 to 4 by @dependabot in #169
• Bump clsx from 1.2.1 to 2.0.0 in /website by @dependabot in #180

Full Changelog: 2022.3.6...v2023.12.0

2022.3.6

What's Changed

• Fix bug in grid search
  The parameters that are fitted when evaluating a grid point were not
  updated. In particular, after the grid search was done, the parameters
  to the best grid point were not returned.
• Bump rich from 13.3.4 to 13.3.5 by @dependabot in #136
• Bump pre-commit from 3.2.2 to 3.3.1 by @dependabot in #137
• Bump lmfit from 1.2.0 to 1.2.1 by @dependabot in #138
• Bump pre-commit from 3.3.1 to 3.3.2 by @dependabot in #141
• Bump eslint from 8.39.0 to 8.41.0 in /website by @dependabot in #142
• Bump cachetools from 5.3.0 to 5.3.1 by @dependabot in #143
• Bump pydantic from 1.10.7 to 1.10.8 by @dependabot in #144
• Bump @docusaurus/core from 2.4.0 to 2.4.1 in /website by @dependabot in #145
• Bump rich from 13.3.5 to 13.4.1 by @dependabot in #146
• Bump rapidfuzz from 3.0.0 to 3.1.0 by @dependabot in #147
• Bump pydantic from 1.10.8 to 1.10.9 by @dependabot in #148
• Bump rich from 13.4.1 to 13.4.2 by @dependabot in #149
• Bump rapidfuzz from 3.1.0 to 3.1.1 by @dependabot in #150
• Bump @docusaurus/eslint-plugin from 2.4.0 to 2.4.1 in /website by @dependabot in #152
• Bump pre-commit from 3.3.2 to 3.3.3 by @dependabot in #153
• Bump numpy from 1.24.3 to 1.25.0 by @dependabot in #154
• Move to ruff by @gbouvignies in #158
• Bump eslint from 8.41.0 to 8.44.0 in /website by @dependabot in #159
• Bump to pydantic v2 by @gbouvignies in #162
• Refactor: Migrate from Poetry to PDM by @gbouvignies in #163
• Refactor for pydantic v2 and better typing by @gbouvignies in #165

Full Changelog: v2022.3.5...2022.3.6

v2022.3.5

What's Changed

• Fix the 3st_eyring model
• Bump numpy from 1.24.2 to 1.24.3 by @dependabot in #131
• Bump eslint from 8.38.0 to 8.39.0 in /website by @dependabot in #132

Full Changelog: v2022.3.4...v2022.3.5

v2022.3.4

Full Changelog: v2022.3.3...v2022.3.4

• Fix a bug when correcting the spin system name
• Update the doc of the 1HN CPMG experiments

v2022.3.3

Full Changelog: v2022.3.2...v2022.3.3

• Bump docusaurus and rapidfuzz version

v2022.3.2

Full Changelog: v2022.3.1...v2022.3.2

• Add pre- and post-equilibration delays in 1H CPMG
• Fix a bug when all parameters were fixed in simul
• Correct a bug in the correction of profile names

v2022.3.1

What's Changed

• Fix parameter estimations using MF parameter
• Fix a bug in cpmg_1hn_ap_0013
• Bump markdown-it-py from 2.1.0 to 2.2.0 by @dependabot in #105
• Bump eslint from 8.34.0 to 8.35.0 in /website by @dependabot in #106
• Bump pre-commit from 2.21.0 to 3.1.1 by @dependabot in #107
• Bump rich from 13.3.1 to 13.3.2 by @dependabot in #108
• Bump matplotlib from 3.7.0 to 3.7.1 by @dependabot in #109
• Bump types-cachetools from 4.2.10 to 5.3.0.4 by @dependabot in #110
• Bump pydantic from 1.10.5 to 1.10.6 by @dependabot in #111
• Bump eslint from 8.35.0 to 8.36.0 in /website by @dependabot in #112
• Bump webpack from 5.73.0 to 5.76.1 in /website by @dependabot in #113
• Bump pre-commit from 3.1.1 to 3.2.0 by @dependabot in #114
• Bump types-cachetools from 5.3.0.4 to 5.3.0.5 by @dependabot in #115
• Bump rich from 13.3.2 to 13.3.3 by @dependabot in #116
• Bump @docusaurus/preset-classic from 2.3.1 to 2.4.0 in /website by @dependabot in #117
• Bump pre-commit from 3.2.0 to 3.2.1 by @dependabot in #118
• Bump @docusaurus/eslint-plugin from 2.3.1 to 2.4.0 in /website by @dependabot in #119
• Bump pydantic from 1.10.6 to 1.10.7 by @dependabot in #120
• Bump pre-commit from 3.2.1 to 3.2.2 by @dependabot in #121
• Bump rapidfuzz from 2.13.7 to 2.15.0 by @dependabot in #122
• Bump eslint from 8.36.0 to 8.37.0 in /website by @dependabot in #123
• Bump lmfit from 1.1.0 to 1.2.0 by @dependabot in #124
• Bump eslint from 8.37.0 to 8.38.0 in /website by @dependabot in #125

Full Changelog: v2022.3.0...v2022.3.1

v2022.3.0

What's Changed

Add two kinetic models for binding reactions

This commits adds new kinetic models for two binding mechanisms.

• '3st_induced_fit' models a binding event followed by a change of
  conformation. The binding event parameters are a dissociation
  constant "KD_AB" and an off-rate "KOFF_AB". The change of
  conformation is modeled using two kinetic rate constants: "KBC" and
  "KCB".
• '3st_double_binding" models a fork model where a protein can bind
  its partner in two different ways. The parameters of the binding
  event AB (AC) are a dissociation constant "KD_AB" ("KD_AC") and an
  off-rate "KOFF_AB" ("KOFF_AC").

The two models require two parameters, "p_total" and "l_total", to be
specified in the conditions.

Add a 15N SQ shift experiment

• Bump loader-utils from 2.0.2 to 2.0.4 in /website by @dependabot in #77
• Bump json5 from 2.2.1 to 2.2.3 in /website by @dependabot in #79
• Bump minimatch, recursive-readdir and serve-handler in /website by @dependabot in #80
• Bump ua-parser-js from 0.7.31 to 0.7.33 in /website by @dependabot in #82
• Bump http-cache-semantics from 4.1.0 to 4.1.1 in /website by @dependabot in #83
• Bump @sideway/formula from 3.0.0 to 3.0.1 in /website by @dependabot in #84
• Bump eta, @docusaurus/core and @docusaurus/preset-classic in /website by @dependabot in #85
• Bump future from 0.18.2 to 0.18.3 by @dependabot in #86
• Bump actions/checkout from 2 to 3 by @dependabot in #87
• Bump actions/setup-python from 3 to 4 by @dependabot in #88
• Bump eslint from 8.23.1 to 8.33.0 in /website by @dependabot in #90
• Bump hast-util-is-element from 1.1.0 to 2.1.3 in /website by @dependabot in #91
• Bump numpy from 1.24.1 to 1.24.2 by @dependabot in #94
• Bump eslint-plugin-react from 7.31.8 to 7.32.2 in /website by @dependabot in #92
• Bump @docusaurus/eslint-plugin from 2.1.0 to 2.3.1 in /website by @dependabot in #93
• Bump cachetools from 5.2.0 to 5.3.0 by @dependabot in #95
• Bump matplotlib from 3.6.2 to 3.6.3 by @dependabot in #96
• Bump rich from 13.0.0 to 13.3.1 by @dependabot in #97
• Bump matplotlib from 3.6.3 to 3.7.0 by @dependabot in #98
• Bump pydantic from 1.10.4 to 1.10.5 by @dependabot in #101
• Bump scipy from 1.10.0 to 1.10.1 by @dependabot in #102
• Bump eslint from 8.33.0 to 8.34.0 in /website by @dependabot in #103

Full Changelog: v2022.2.0...v2022.3.0

v2022.2.0

What's changed

Add models using temperature coefficients

Chemical shifts are now temperature-dependant. In addition, in
temperature dependant models, such as 2st_eyring, it is now possible
to use temperature coefficient by adding the extension .tc to the
model name, eg 2st_eyring.tc.

When temperature coefficients are used, the following relationship
holds:

DW_AB = DWM_AB * T + DWP_AB

where DWM_AB is the temperature coefficient in ppm/ºC, DWP_AB is the
chemical shift difference between A and B at 0ºC in ppm, and T is the
temperature in Celsius. DWM_AB and DWP_AB are fitted and
temperature-independant.

Correct the simulation module

The simulation module was broken: depending on the values given in the
fake profiles, that are necessary to run the simulation, the
back-calculated R2 values were offset differently. This is now fixed.

The calculated profiles are also available in the Data directory.

Correct incorrect 'kij' calculation

Full Changelog: v2022.1.0...v2022.2.0

v2022.1.0

What's Changed

Refactor the code related to the kinetic models
A new plugin architecture has been implemented to facilitate the addition of new kinetic models. The code for calculating some of the
constrained rates and populations have been changed to use some optimization calculation instead of an analytical formula (when possible and when the analytical formula is more complicated to read).

'New' kinetic models have been added:

• "3st_linear": A <-> B <-> C
• "3st_fork": C <-> A <-> B
• "3st_triangle": identical to "3st"
• "2st_a_a2": 2*A <-> A2
• "2st_a_a3": 3*A <-> A3
• "2st_a_a4": 4*A <-> A4
• "3st_a_a2_a3": 2*A <-> A2, A+A2 <-> A3
• "3st_a_a2_a4": 2A <-> A2, 2A2 <-> A4

Full Changelog: v2022.0.1...v2022.1.0