From 0e3b5a9ec3fec9bdb7f68ed8eeaa4ecc4dc0db22 Mon Sep 17 00:00:00 2001 From: David Seiferth Date: Tue, 8 Oct 2024 11:22:49 +0100 Subject: [PATCH 1/6] add PoreAnalyser --- mdakits/PoreAnalyser | 1 + 1 file changed, 1 insertion(+) create mode 160000 mdakits/PoreAnalyser diff --git a/mdakits/PoreAnalyser b/mdakits/PoreAnalyser new file mode 160000 index 00000000..6cf49f66 --- /dev/null +++ b/mdakits/PoreAnalyser @@ -0,0 +1 @@ +Subproject commit 6cf49f668b9501c2b9533822e0798b183efb1c95 From d1fcd4c6d2aaa4ce52acc16743a92e31dba5dbed Mon Sep 17 00:00:00 2001 From: David Seiferth Date: Tue, 8 Oct 2024 11:28:46 +0100 Subject: [PATCH 2/6] del --- mdakits/PoreAnalyser | 1 - 1 file changed, 1 deletion(-) delete mode 160000 mdakits/PoreAnalyser diff --git a/mdakits/PoreAnalyser b/mdakits/PoreAnalyser deleted file mode 160000 index 6cf49f66..00000000 --- a/mdakits/PoreAnalyser +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 6cf49f668b9501c2b9533822e0798b183efb1c95 From 938904cc3a0f0fb8d073986b116e403b99891885 Mon Sep 17 00:00:00 2001 From: David Seiferth Date: Tue, 8 Oct 2024 12:18:12 +0100 Subject: [PATCH 3/6] add metadata --- mdakits/PoreAnalyser/metadata.yaml | 71 ++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 mdakits/PoreAnalyser/metadata.yaml diff --git a/mdakits/PoreAnalyser/metadata.yaml b/mdakits/PoreAnalyser/metadata.yaml new file mode 100644 index 00000000..59c0c354 --- /dev/null +++ b/mdakits/PoreAnalyser/metadata.yaml @@ -0,0 +1,71 @@ +project_name: PoreAnalyser + +authors: + - David Seiferth + +maintainers: + - DSeiferth + - philbiggin + +description: + PoreAnalyser is a Python library for analysing (ion channel) pore profiles. We introduce an algorithm that employs + ellipsoidal probe particles, enabling a more comprehensive characterization of pore asymmetries. A constriction is + more asymmetric for a larger difference between the smaller and larger radius of the ellipsoidal probe particle. + Furthermore, we make use of the more accurate characterization of channel pores to refine a physical conductance + model to obtain a heuristic estimate for single-channel conductance. + +keywords: + - channels + - conductance + - pore + +## See https://spdx.org/licenses/ for valid license specifiers +license: LGPL-2.1-only + +project_home: https://github.com/DSeiferth/PoreAnalyser + +documentation_home: https://porefinding.readthedocs.io/en/latest/?badge=latest + +## str: the type of documentation available [UserGuide, API, README] +documentation_type: UserGuide + API + README + +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/DSeiferth/PoreAnalyser@main + +import_name: PoreAnalyser + +python_requires: ">=3.9" + +mdanalysis_requires: ">=2.0.0" + +run_tests: +# - pytest --pyargs MYPACKAGE + - git clone latest + - cd PoreAnalyser # tests are in PoreAnalyser/tests/ + - python -m unittest discover + +## List(str): a list of commands to use to install the necessary dependencies required +## to run the MDAKit's tests. +## The default below _might_ be sufficient or you might not even need MDAnalysisTests: +## make sure that it is appropriate for how you run tests. +test_dependencies: + - mamba install pytest MDAnalysisTests + +## str: the organisation name the MDAKit falls under +project_org: DSeiferth + +#------------------------------------------------------------ +# Optional entries +#------------------------------------------------------------ +install: + - pip install PoreAnalyser + +## str: the development status of the MDAKit +## See https://pypi.org/classifiers/ for development status classifiers. +#development_status: Production/Stable + +publications: + - https://doi.org/10.1016/j.bpj.2024.07.010 + From 5f2cd3d60c6d0078cbece6c74a6f24266c44cb3a Mon Sep 17 00:00:00 2001 From: David Seiferth Date: Wed, 16 Oct 2024 12:56:48 +0100 Subject: [PATCH 4/6] changes from pull request --- mdakits/PoreAnalyser/metadata.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mdakits/PoreAnalyser/metadata.yaml b/mdakits/PoreAnalyser/metadata.yaml index 59c0c354..573f07de 100644 --- a/mdakits/PoreAnalyser/metadata.yaml +++ b/mdakits/PoreAnalyser/metadata.yaml @@ -24,7 +24,7 @@ license: LGPL-2.1-only project_home: https://github.com/DSeiferth/PoreAnalyser -documentation_home: https://porefinding.readthedocs.io/en/latest/?badge=latest +documentation_home: https://porefinding.readthedocs.io ## str: the type of documentation available [UserGuide, API, README] documentation_type: UserGuide + API + README @@ -50,8 +50,8 @@ run_tests: ## to run the MDAKit's tests. ## The default below _might_ be sufficient or you might not even need MDAnalysisTests: ## make sure that it is appropriate for how you run tests. -test_dependencies: - - mamba install pytest MDAnalysisTests +#test_dependencies: +# - mamba install pytest MDAnalysisTests ## str: the organisation name the MDAKit falls under project_org: DSeiferth From 62f866b9ed28fcfa72bfbe1c24e7e721f5b6355d Mon Sep 17 00:00:00 2001 From: David Seiferth Date: Wed, 16 Oct 2024 13:04:07 +0100 Subject: [PATCH 5/6] change liscene to or later --- mdakits/PoreAnalyser/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/PoreAnalyser/metadata.yaml b/mdakits/PoreAnalyser/metadata.yaml index 573f07de..aba7b603 100644 --- a/mdakits/PoreAnalyser/metadata.yaml +++ b/mdakits/PoreAnalyser/metadata.yaml @@ -20,7 +20,7 @@ keywords: - pore ## See https://spdx.org/licenses/ for valid license specifiers -license: LGPL-2.1-only +license: LGPL-2.1-or-later project_home: https://github.com/DSeiferth/PoreAnalyser From 5ade7c8768f549e855dca362a1900ed05925c14d Mon Sep 17 00:00:00 2001 From: David Seiferth <72927167+DSeiferth@users.noreply.github.com> Date: Fri, 18 Oct 2024 23:59:16 +0200 Subject: [PATCH 6/6] Update mdakits/PoreAnalyser/metadata.yaml Co-authored-by: Oliver Beckstein --- mdakits/PoreAnalyser/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/mdakits/PoreAnalyser/metadata.yaml b/mdakits/PoreAnalyser/metadata.yaml index aba7b603..bb5aaba4 100644 --- a/mdakits/PoreAnalyser/metadata.yaml +++ b/mdakits/PoreAnalyser/metadata.yaml @@ -41,7 +41,6 @@ python_requires: ">=3.9" mdanalysis_requires: ">=2.0.0" run_tests: -# - pytest --pyargs MYPACKAGE - git clone latest - cd PoreAnalyser # tests are in PoreAnalyser/tests/ - python -m unittest discover