From 8a74a7d1f07f2476c13067d6d7168f795d916a4b Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Thu, 22 Jun 2023 10:58:22 +0200 Subject: [PATCH 1/7] Typo in fitting guide --- docsrc/source/fitting_guide.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docsrc/source/fitting_guide.rst b/docsrc/source/fitting_guide.rst index fc81f13e..483a5348 100644 --- a/docsrc/source/fitting_guide.rst +++ b/docsrc/source/fitting_guide.rst @@ -66,7 +66,7 @@ Fitting multi-dataset models Models merged using the ``merge`` function (see :ref:`here ` for details) can describe multiple datasets with a single model object and a common parameter set. To fit such a merged model to multiple datasets, the ``fit`` function can be used as above by passing a list of datasets ``[y1,y2,...,yN]`` instead of a single dataset :: # Fit the model to multiple datasets - result = dl.fit(model, [y1,y2,y3] + result = dl.fit(model, [y1,y2,y3]) The number of datasets must match the number of responses returned by the model. Additionally, the ordering in the list of datasets must match the order of responses from the model, i.e. ``response1`` of ``model`` will be fitted to ``y1``, and so on. From bec71770cc60aa71db6b472a7bc27d17ddf7fce2 Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Wed, 28 Jun 2023 15:58:27 +0200 Subject: [PATCH 2/7] Fixed time axis on crossing echo example --- examples/intermediate/ex_crossing_echoes_masking.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/examples/intermediate/ex_crossing_echoes_masking.py b/examples/intermediate/ex_crossing_echoes_masking.py index de7796a9..db2cba66 100644 --- a/examples/intermediate/ex_crossing_echoes_masking.py +++ b/examples/intermediate/ex_crossing_echoes_masking.py @@ -27,6 +27,8 @@ # Load the experimental data t,Vexp = dl.deerload('../data/example_4pdeer_5.DTA') +t *= 1e3 # convert from ms to us + # Experimental parameters tau1 = 0.5 # First inter-pulse time delay, μs tau2 = 4.5 # Second inter-pulse time delay, μs From b1190ec6a2ebdbf591aa4506788c62288d50c3a3 Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Mon, 24 Jul 2023 14:54:23 +0200 Subject: [PATCH 3/7] Remove default font --- deerlab/solvers.py | 1 - 1 file changed, 1 deletion(-) diff --git a/deerlab/solvers.py b/deerlab/solvers.py index 845c56ef..fa67edd5 100644 --- a/deerlab/solvers.py +++ b/deerlab/solvers.py @@ -136,7 +136,6 @@ def _plot(ys,yfits,yuqs,noiselvls,axis=None,xlabel=None,gof=False,fontsize=13): # Adjust fontsize for ax in axs: for label in (ax.get_xticklabels() + ax.get_yticklabels()): - label.set_fontname('Calibri') label.set_fontsize(fontsize) return fig From 6c314d06e600f4a5fc0dea4265634107ceb8a070 Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Mon, 24 Jul 2023 15:00:11 +0200 Subject: [PATCH 4/7] Expand search range in `test_algorithms` --- test/test_selregparam.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_selregparam.py b/test/test_selregparam.py index e50f70c1..ef9b8837 100644 --- a/test/test_selregparam.py +++ b/test/test_selregparam.py @@ -53,8 +53,8 @@ def test_selection_criteria_values(dataset, design_matrix, regularization_matrix #======================================================================= def test_algorithms(dataset, design_matrix, regularization_matrix): "Check that the value returned by the the grid and Brent algorithms coincide" - alpha_grid = selregparam(dataset,design_matrix,qpnnls,method='aic',algorithm='grid',regop=regularization_matrix) - alpha_brent = selregparam(dataset,design_matrix,qpnnls,method='aic',algorithm='brent',regop=regularization_matrix) + alpha_grid = selregparam(dataset,design_matrix,qpnnls,method='aic',algorithm='grid',regop=regularization_matrix, searchrange=[1e-10,1e-6]) + alpha_brent = selregparam(dataset,design_matrix,qpnnls,method='aic',algorithm='brent',regop=regularization_matrix, searchrange=[1e-10,1e-6]) assert abs(1-alpha_grid/alpha_brent) < 0.2 #======================================================================= From 4422141179d82603df24cfc8394033addd5013fe Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Mon, 24 Jul 2023 15:03:58 +0200 Subject: [PATCH 5/7] Rename files to American English spelling --- ...ide_graphics.svg => modeling_guide_graphics.svg} | 0 ...lincombine.png => modeling_guide_lincombine.png} | Bin ...ncombine1.png => modeling_guide_lincombine1.png} | Bin ...ncombine2.png => modeling_guide_lincombine2.png} | Bin ...lling_guide_link.png => modeling_guide_link.png} | Bin ...ing_guide_merge.png => modeling_guide_merge.png} | Bin ...g_guide_relate.png => modeling_guide_relate.png} | Bin 7 files changed, 0 insertions(+), 0 deletions(-) rename docsrc/source/images/{modelling_guide_graphics.svg => modeling_guide_graphics.svg} (100%) rename docsrc/source/images/{modelling_guide_lincombine.png => modeling_guide_lincombine.png} (100%) rename docsrc/source/images/{modelling_guide_lincombine1.png => modeling_guide_lincombine1.png} (100%) rename docsrc/source/images/{modelling_guide_lincombine2.png => modeling_guide_lincombine2.png} (100%) rename docsrc/source/images/{modelling_guide_link.png => modeling_guide_link.png} (100%) rename docsrc/source/images/{modelling_guide_merge.png => modeling_guide_merge.png} (100%) rename docsrc/source/images/{modelling_guide_relate.png => modeling_guide_relate.png} (100%) diff --git a/docsrc/source/images/modelling_guide_graphics.svg b/docsrc/source/images/modeling_guide_graphics.svg similarity index 100% rename from docsrc/source/images/modelling_guide_graphics.svg rename to docsrc/source/images/modeling_guide_graphics.svg diff --git a/docsrc/source/images/modelling_guide_lincombine.png b/docsrc/source/images/modeling_guide_lincombine.png similarity index 100% rename from docsrc/source/images/modelling_guide_lincombine.png rename to docsrc/source/images/modeling_guide_lincombine.png diff --git a/docsrc/source/images/modelling_guide_lincombine1.png b/docsrc/source/images/modeling_guide_lincombine1.png similarity index 100% rename from docsrc/source/images/modelling_guide_lincombine1.png rename to docsrc/source/images/modeling_guide_lincombine1.png diff --git a/docsrc/source/images/modelling_guide_lincombine2.png b/docsrc/source/images/modeling_guide_lincombine2.png similarity index 100% rename from docsrc/source/images/modelling_guide_lincombine2.png rename to docsrc/source/images/modeling_guide_lincombine2.png diff --git a/docsrc/source/images/modelling_guide_link.png b/docsrc/source/images/modeling_guide_link.png similarity index 100% rename from docsrc/source/images/modelling_guide_link.png rename to docsrc/source/images/modeling_guide_link.png diff --git a/docsrc/source/images/modelling_guide_merge.png b/docsrc/source/images/modeling_guide_merge.png similarity index 100% rename from docsrc/source/images/modelling_guide_merge.png rename to docsrc/source/images/modeling_guide_merge.png diff --git a/docsrc/source/images/modelling_guide_relate.png b/docsrc/source/images/modeling_guide_relate.png similarity index 100% rename from docsrc/source/images/modelling_guide_relate.png rename to docsrc/source/images/modeling_guide_relate.png From 38f4625a9de26ce936eb01eacb34ec9348e1bda6 Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Mon, 24 Jul 2023 15:22:11 +0200 Subject: [PATCH 6/7] Update Changelog --- docsrc/source/changelog.rst | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/docsrc/source/changelog.rst b/docsrc/source/changelog.rst index 78d1fab2..006fe0fc 100644 --- a/docsrc/source/changelog.rst +++ b/docsrc/source/changelog.rst @@ -14,6 +14,35 @@ Release Notes - |fix| : Something which was not working as expected or leading to errors has been fixed. - |api| : This will require changes in your scripts or code. +Release ``v1.0.2`` - July 2023 +------------------------------------------ +- |fix| : Fixes errors in documentation (:pr:`429`). + + * Changes the file name of figures 'modelling*.png` to `modeling*.png`. To keep all spelling consistent with american english. + * Adds a missing `)` in `fitting_guide` + * Corrects the time axis in `echo_crossing` example. + +- |fix| : Fixes an errors in tests (:pr:`429`). + + * The test `test_algorithms` had an incorrect search range. + +- |fix| : Removes the default font from the `fit` function due to conflicts on some systems (:pr:`429`). + +Release ``v1.0.1`` - March 2023 +------------------------------------------ +- |fix| : Fixes some minor bugs in the documentation. + + * The file modelling_guide.rst is renamed to modeling_guide.rst to keep spelling consistency. + * The "Simulating a two-pathway 5-pulse DEER signal" and "Simulating a three-pathway 4-pulse DEER signal" examples now run correctly. + * +- |fix| : Fixes issues with CVXOPT in tests. + + * The testing will now use quadprog as the default solver. To account for the change tested values are now generated using the grid method + +- |fix| : Updates GitHub actions to use latest packages. +- |api| : Hardcodes out Python 3.11 support. This will remain until quadprog is fixed. +- |api| : Removes hard-wired RNG seeding + Release ``v1.0.0`` - December 2022 ------------------------------------------ From 24e5d1fecabeb5c505c58a4411f52234913dc1d6 Mon Sep 17 00:00:00 2001 From: Hugo Karas Date: Mon, 24 Jul 2023 15:29:14 +0200 Subject: [PATCH 7/7] Update version number --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 0ec25f75..570c7965 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v1.0.0 +v1.0.2