From 766c63b638e8b1247c0a42dff9fd2758488ce935 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Oct 2024 21:17:53 +0100 Subject: [PATCH 1/3] Add poreanalyzer --- mdakits/poreanalyzer/metadata.yaml | 70 ++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 mdakits/poreanalyzer/metadata.yaml diff --git a/mdakits/poreanalyzer/metadata.yaml b/mdakits/poreanalyzer/metadata.yaml new file mode 100644 index 00000000..9851e4e3 --- /dev/null +++ b/mdakits/poreanalyzer/metadata.yaml @@ -0,0 +1,70 @@ +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 53f518e2bab62fed4ec37548b7089544d29bb9e1 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Oct 2024 21:20:06 +0100 Subject: [PATCH 2/3] bump up miniconda setup action --- .github/workflows/gh-ci-cron.yaml | 2 +- .github/workflows/gh-ci.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 614b4c50..08f85936 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -79,7 +79,7 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index f320aa1a..d7258a17 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -82,7 +82,7 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true From 8b70dee5f40ec9f679aef497f7b8244d08e77563 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Oct 2024 21:24:33 +0100 Subject: [PATCH 3/3] switch to miniforge --- .github/workflows/gh-ci-cron.yaml | 2 +- .github/workflows/gh-ci.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 08f85936..829f654c 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -85,7 +85,7 @@ jobs: add-pip-as-python-dependency: true architecture: x64 use-mamba: true - miniforge-variant: Mambaforge + miniforge-version: latest channels: conda-forge, defaults channel-priority: flexible auto-update-conda: true diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index d7258a17..279c2110 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -88,7 +88,7 @@ jobs: add-pip-as-python-dependency: true architecture: x64 use-mamba: true - miniforge-variant: Mambaforge + miniforge-version: latest channels: conda-forge, defaults channel-priority: flexible auto-update-conda: true