From daf401db473f49f218acc30f3b12454d30135628 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:22:07 -0400 Subject: [PATCH 1/5] Clean up index.rst with redundant info --- doc/source/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 735ea36..0a1bc3f 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -2,7 +2,7 @@ Welcome to SNMF's Documentation! ==================================== ``SNMF``: This library implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF -(ssNMF) algorithms described in ... +(ssNMF) algorithms. This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal on the independent variable axis. For example, for powder diffraction data taken from samples containing multiple @@ -54,7 +54,7 @@ by citing the following paper in your publication: Authors ------- -``snmf`` implements the algorithms described in ...., developed by members of the Billinge Group at +``diffpy.snmf`` is developed by members of the Billinge Group at Columbia University, Brookhaven National Laboratory, Stony Brook University, Nankai University, and Colorado State University including Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O'Nolan, Brennan Mcbride, Jame R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge. From 1e5050daea60f76c7a1dc4585602aa16ba56b423 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:24:12 -0400 Subject: [PATCH 2/5] Add package description in README.rst --- README.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index b3b8833..2d9c0dc 100644 --- a/README.rst +++ b/README.rst @@ -37,7 +37,10 @@ A python package implementing the stretched NMF algorithm. -* LONGER DESCRIPTION HERE +``diff.pysnmf`` is a Python package that increases the insight one can obtain from a measured series time-dependent signals +through applying the stretched nonnegative matrix factorization (sNMF) and spare stretched nonnegative matrix factorization +algorithms (ssNMF). The package seeks to answer the question: "What are the structural signals composing my measured signal at +each moment in time?" For more information about the diffpy.snmf library, please consult our `online documentation `_. From 50bf2fddd42c38e601677f2cf66029e2dd7b9057 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 08:28:19 -0400 Subject: [PATCH 3/5] Fix typo from diff.pysnmf to diffpy.snmf --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 2d9c0dc..f1e47ca 100644 --- a/README.rst +++ b/README.rst @@ -37,7 +37,7 @@ A python package implementing the stretched NMF algorithm. -``diff.pysnmf`` is a Python package that increases the insight one can obtain from a measured series time-dependent signals +``diffpy.snmf`` is a Python package that increases the insight one can obtain from a measured series time-dependent signals through applying the stretched nonnegative matrix factorization (sNMF) and spare stretched nonnegative matrix factorization algorithms (ssNMF). The package seeks to answer the question: "What are the structural signals composing my measured signal at each moment in time?" From 4bc33e7aa9b64d5e86dbc94b58d9ebe3a098d088 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 19:00:17 -0400 Subject: [PATCH 4/5] Update REAMDE longer description --- README.rst | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index f1e47ca..aa574de 100644 --- a/README.rst +++ b/README.rst @@ -37,10 +37,13 @@ A python package implementing the stretched NMF algorithm. -``diffpy.snmf`` is a Python package that increases the insight one can obtain from a measured series time-dependent signals -through applying the stretched nonnegative matrix factorization (sNMF) and spare stretched nonnegative matrix factorization -algorithms (ssNMF). The package seeks to answer the question: "What are the structural signals composing my measured signal at -each moment in time?" +``diffpy.snmf`` implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF +(ssNMF) algorithms. + +This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal +on the independent variable axis. For example, for powder diffraction data taken from samples containing multiple +chemical phases where the measurements were done at different temperatures and the materials were undergoing thermal +expansion. For more information about the diffpy.snmf library, please consult our `online documentation `_. From 5446afd4a874ab4efcb5330fc97e4d42710b3ef1 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 12 Aug 2024 19:59:50 -0400 Subject: [PATCH 5/5] Make a clear ref to the paper in readme --- doc/source/index.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 0a1bc3f..1122b4f 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -2,7 +2,8 @@ Welcome to SNMF's Documentation! ==================================== ``SNMF``: This library implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF -(ssNMF) algorithms. +(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023), +which is referenced under the Citation section below. This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal on the independent variable axis. For example, for powder diffraction data taken from samples containing multiple @@ -54,7 +55,7 @@ by citing the following paper in your publication: Authors ------- -``diffpy.snmf`` is developed by members of the Billinge Group at +``snmf`` implements the algorithms described in ...., developed by members of the Billinge Group at Columbia University, Brookhaven National Laboratory, Stony Brook University, Nankai University, and Colorado State University including Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O'Nolan, Brennan Mcbride, Jame R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge.