From 61210f7aabb7b995d79ac264243d49359d618669 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 15:18:54 -0500 Subject: [PATCH 01/15] Update to python 3.12 and MDA 2.8 (LGPL) --- .github/workflows/python-package-conda.yml | 4 +- docs/about.rst | 10 ++--- docs/conf.py | 2 +- docs/installation.rst | 2 +- docs/requirements.txt | 12 +++--- docs/tut-2-preprocessing.rst | 44 +++++++++++++--------- environment.yml | 15 ++++---- setup.py | 12 +++--- 8 files changed, 56 insertions(+), 45 deletions(-) diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index cfe752d..0bc4d8d 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -12,10 +12,10 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v3 - - name: Set up Python 3.9 + - name: Set up Python 3.12 uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: 3.12 - name: Lint with flake8 run: | pip install flake8 diff --git a/docs/about.rst b/docs/about.rst index c38fcd9..404de57 100644 --- a/docs/about.rst +++ b/docs/about.rst @@ -27,14 +27,14 @@ All functionality is available as a python package. Citation ******** -If you publish about work for which PENSA was useful, please cite our preprint: +If you publish about work for which PENSA was useful, please cite our publication: - M. Vögele, N. J. Thomson, S. T. Truong, J. McAvity, U. Zachariae, R. O. Dror: - *Systematic Analysis of Biomolecular Conformational Ensembles with PENSA*. - `arXiv:2212.02714 [q-bio.BM] 2022 `_. + M. Vögele, N. J. Thomson, S. T. Truong, J. McAvity, U. Zachariae, R. O. Dror: + *Systematic analysis of biomolecular conformational ensembles with PENSA*. + `J. Chem. Phys. 162, 014101 (2025) `_. The reference for the software implementation itself is the following: - Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity: *PENSA*. Zenodo, 2024. http://doi.org/10.5281/zenodo.4362136 + Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity: *PENSA*. Zenodo, 2025. http://doi.org/10.5281/zenodo.4362136 To get the citation and DOI for a particular version, see `Zenodo `_. diff --git a/docs/conf.py b/docs/conf.py index 6162527..3d0748f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -21,7 +21,7 @@ # -- Project information ----------------------------------------------------- project = 'PENSA' -copyright = '2020-2024, Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity' +copyright = '2020-2025, Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity' author = 'Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity' diff --git a/docs/installation.rst b/docs/installation.rst index 411674a..5e16940 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -8,7 +8,7 @@ Create and activate a conda environment: .. code:: bash - conda create --name pensa python=3.9 numpy==1.22 scipy==1.9 pandas==1.4 matplotlib==3.5 MDAnalysis==2.2 cython biotite -c conda-forge -c conda-forge + conda create --name pensa python==3.12 scipy numpy pandas matplotlib MDAnalysis==2.8 deeptime biotite pip==24 -c conda-forge conda activate pensa If you want to use PENSA with Jupyter notebooks: diff --git a/docs/requirements.txt b/docs/requirements.txt index 523dada..8240fda 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -7,12 +7,12 @@ sphinxcontrib-htmlhelp sphinxcontrib-jsmath sphinxcontrib-qthelp sphinxcontrib-serializinghtml -numpy==1.22 -scipy==1.9 -pandas==1.4 -matplotlib==3.5 +numpy +scipy +pandas +matplotlib deeptime -MDAnalysis==2.2 +MDAnalysis==2.8 cython biotite -pensa==0.3.0 +pensa diff --git a/docs/tut-2-preprocessing.rst b/docs/tut-2-preprocessing.rst index 1f70a16..eff32d7 100644 --- a/docs/tut-2-preprocessing.rst +++ b/docs/tut-2-preprocessing.rst @@ -10,19 +10,19 @@ Preprocessing extract_aligned_coordinates, extract_combined_grid -Coordinates -*********** +To work with the biomolecule's coordinates, it is often easier to first extract +them from the simulation, i.e., remove the solvent, lipids etc. If you would like +to calculate water or ion features, you need to calculate the corresponding density. +This kind of preprocessing steps can be cumbersome but you usually only do it +once and can then play with your data. -To work with the biomolecule's coordinates, we first need to extract them from -the simulation, i.e., remove the solvent, lipids etc. This is the hardest part -but you usually only have to do it once and can then play with your data. -Preprocessing can handle many common trajectory formats as it is based on -MDAnalysis. You can start by using the scripts provided in the PENSA repository. -Once you know how PENSA works, you can write your own scripts. +Based on MDAnalysis, PENSA's preprocessing functions can handle many common formats +of molecular simulation trajectories. You can start by using the scripts provided +in the PENSA repository. Once you know how PENSA works, you can write your own scripts. Files and Directories ---------------------- +********************** In the following, we define the necessary files. For each simulation, we need a reference file (.psf for AMBER), a PDB file, and the trajetory. @@ -71,8 +71,8 @@ will generate. os.makedirs(subdir) -Extracting Coordinates ----------------------- +Coordinates +*********** We have to ensure that from both simulations, we use the exact same parts of the receptor for the analysis. Often, this will be easy and you @@ -91,14 +91,24 @@ In the first case, we will extract all protein residues, assuming extract_coordinates(ref_file_a, pdb_file_a, trj_file_a, out_name_a+"_receptor", sel_base_a) extract_coordinates(ref_file_b, pdb_file_b, trj_file_b, out_name_b+"_receptor", sel_base_b) -In many cases, you probably have several runs of the same simulation -that you want to combine to one structural ensemble. This is why the -trajectory argument takes a list as arguments, e.g. +In some cases, you may have only one trajectory while in others, +you may have several runs of the same simulation that you want +to combine to one structural ensemble. +This is why the trajectory argument can be either a single string + +.. code:: python + + extract_coordinates( + 'system.psf', 'system.pdb', 'run1.nc', + 'receptor', 'protein', start_frame=1000 + ) + +... or a list of strings. .. code:: python extract_coordinates( - 'system.psf', 'system.pdb', ['run1.nc','run2.nc','run3.nc'], + 'system.psf', 'system.pdb', ['run1.nc','run2.nc','run3.nc'], 'receptor', 'protein', start_frame=1000 ) @@ -129,8 +139,8 @@ Here, we use selections based on the definitions of transmembrane helices in the sel_string_b = "protein and resnum "+resnums print('Selection B:\n', sel_string_b, '\n') # Extract the coordinates of the transmembrane region from the trajectory - extract_coordinates(ref_file_a, pdb_file_a, [trj_file_a], out_name_a+"_tm", sel_string_a) - extract_coordinates(ref_file_b, pdb_file_b, [trj_file_b], out_name_b+"_tm", sel_string_b) + extract_coordinates(ref_file_a, pdb_file_a, trj_file_a, out_name_a+"_tm", sel_string_a) + extract_coordinates(ref_file_b, pdb_file_b, trj_file_b, out_name_b+"_tm", sel_string_b) Loading from Multiple Simulations diff --git a/environment.yml b/environment.yml index 53d086f..7ab6934 100644 --- a/environment.yml +++ b/environment.yml @@ -1,13 +1,14 @@ -name: pensa +name: pensa_py312 channels: - conda-forge - defaults dependencies: - - python==3.9 - - scipy==1.9 - - numpy==1.22 - - pandas==1.4 - - matplotlib==3.5 - - MDAnalysis==2.2 + - python==3.12 + - scipy + - numpy + - pandas + - matplotlib + - MDAnalysis==2.8 - deeptime - biotite + - pip==24 diff --git a/setup.py b/setup.py index f8ed579..629bef1 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='pensa', - version='0.5.0', + version='0.6.0', description='exploratory analysis and comparison of biomolecular conformational ensembles.', url='http://github.com/drorlab/pensa', author='Martin Voegele, Neil Thomson, Sang Truong, Jasper McAvity', @@ -21,12 +21,12 @@ ), zip_safe=False, install_requires=[ - 'numpy==1.22', # density functions in MDAnalysis 2 use np.histogramdd() with keyword normed which is deprecated in numpy 1.21 and removed in numpy 1.24 - 'scipy==1.9', - 'pandas==1.4', - 'matplotlib==3.5', + 'numpy>=1.23', # density functions in MDAnalysis 2 use np.histogramdd() with keyword normed which is deprecated in numpy 1.21 and removed in numpy 1.24 + 'scipy>=1.15', + 'pandas>=2.2', + 'matplotlib>=3.9', 'deeptime', - 'MDAnalysis==2.2', # some features we use will likely be removed in MDA 3 + 'MDAnalysis==2.8', # some features we use will likely be removed in MDA 3 'biotite', 'gpcrmining', ], From 56a4503a48cc3c262c27ddce2779b2c085c99f97 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 15:19:51 -0500 Subject: [PATCH 02/15] standard environment name --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 7ab6934..a52d778 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: pensa_py312 +name: pensa channels: - conda-forge - defaults From 03615f1d3addb68cc24e7c59fe3fa810a2e2e750 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 15:33:45 -0500 Subject: [PATCH 03/15] reduce version restrictions --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 629bef1..408a8e5 100644 --- a/setup.py +++ b/setup.py @@ -22,9 +22,9 @@ zip_safe=False, install_requires=[ 'numpy>=1.23', # density functions in MDAnalysis 2 use np.histogramdd() with keyword normed which is deprecated in numpy 1.21 and removed in numpy 1.24 - 'scipy>=1.15', - 'pandas>=2.2', - 'matplotlib>=3.9', + 'scipy', + 'pandas', + 'matplotlib', 'deeptime', 'MDAnalysis==2.8', # some features we use will likely be removed in MDA 3 'biotite', From 2149f4750f0ccf1fe0b3d66d1a7c5a8993c4b016 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:12:50 -0500 Subject: [PATCH 04/15] replace setup.py with pyproject.toml --- pyproject.toml | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 44 -------------------------------------- 2 files changed, 57 insertions(+), 44 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..68d8eeb --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,57 @@ +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "pensa" +version = "0.6.0" +description = "exploratory analysis and comparison of biomolecular conformational ensembles." +authors = [ + {name = "Martin Voegele, Neil Thomson, Sang Truong, Jasper McAvity", email = "martinvoegele1989@gmail.com"} +] +license = {text = "MIT"} +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Scientific/Engineering :: Physics", + "Topic :: Scientific/Engineering :: Visualization", + "Topic :: Scientific/Engineering :: Information Analysis", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "Topic :: Scientific/Engineering :: Mathematics", + "Topic :: Scientific/Engineering :: Medical Science Apps.", + "Topic :: Scientific/Engineering :: Molecular Dynamics", + "Topic :: Scientific/Engineering :: Computational Biology", +] +dependencies = [ + "numpy>=1.23", + "scipy", + "pandas", + "matplotlib", + "deeptime", + "MDAnalysis==2.8", + "biotite", + "gpcrmining", +] +requires-python = "==3.12" + +[project.urls] +Documentation = "https://pensa.readthedocs.io/en/latest/" +Source = "http://github.com/drorlab/pensa" + +[tool.setuptools.packages.find] +include = [ + "pensa", + "pensa.preprocessing", + "pensa.features", + "pensa.comparison", + "pensa.dimensionality", + "pensa.clusters", + "pensa.statesinfo" +] + + + diff --git a/setup.py b/setup.py deleted file mode 100644 index 408a8e5..0000000 --- a/setup.py +++ /dev/null @@ -1,44 +0,0 @@ -from setuptools import setup, find_packages - -setup( - name='pensa', - version='0.6.0', - description='exploratory analysis and comparison of biomolecular conformational ensembles.', - url='http://github.com/drorlab/pensa', - author='Martin Voegele, Neil Thomson, Sang Truong, Jasper McAvity', - author_email='martinvoegele1989@gmail.com', - license='MIT', - packages=find_packages( - include=[ - 'pensa', - 'pensa.preprocessing', - 'pensa.features', - 'pensa.comparison', - 'pensa.dimensionality', - 'pensa.clusters', - 'pensa.statesinfo', - ] - ), - zip_safe=False, - install_requires=[ - 'numpy>=1.23', # density functions in MDAnalysis 2 use np.histogramdd() with keyword normed which is deprecated in numpy 1.21 and removed in numpy 1.24 - 'scipy', - 'pandas', - 'matplotlib', - 'deeptime', - 'MDAnalysis==2.8', # some features we use will likely be removed in MDA 3 - 'biotite', - 'gpcrmining', - ], - classifiers=[ - # How mature is this project? Common values are - # 3 - Alpha - # 4 - Beta - # 5 - Production/Stable - 'Development Status :: 4 - Beta', - # license (should match "license" above) - 'License :: OSI Approved :: MIT License', - # Supported Python versions - 'Programming Language :: Python :: 3', - ], -) From bef092e5e156543fc4277047361725cb76c4ac82 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:17:18 -0500 Subject: [PATCH 05/15] use most recent pip --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index a52d778..336f275 100644 --- a/environment.yml +++ b/environment.yml @@ -11,4 +11,4 @@ dependencies: - MDAnalysis==2.8 - deeptime - biotite - - pip==24 + - pip From 0e8d01770f2733570f115a9796d6831e49bdef1e Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:27:52 -0500 Subject: [PATCH 06/15] revert to python 3.10 because of deeptime --- .github/workflows/python-package-conda.yml | 4 ++-- docs/installation.rst | 2 +- environment.yml | 2 +- pyproject.toml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index 0bc4d8d..d982fb5 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -12,10 +12,10 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v3 - - name: Set up Python 3.12 + - name: Set up Python 3.10 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.10 - name: Lint with flake8 run: | pip install flake8 diff --git a/docs/installation.rst b/docs/installation.rst index 5e16940..ec1c637 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -8,7 +8,7 @@ Create and activate a conda environment: .. code:: bash - conda create --name pensa python==3.12 scipy numpy pandas matplotlib MDAnalysis==2.8 deeptime biotite pip==24 -c conda-forge + conda create --name pensa python==3.10 scipy numpy pandas matplotlib MDAnalysis==2.8 deeptime biotite pip -c conda-forge conda activate pensa If you want to use PENSA with Jupyter notebooks: diff --git a/environment.yml b/environment.yml index 336f275..1d98214 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - defaults dependencies: - - python==3.12 + - python==3.10 - scipy - numpy - pandas diff --git a/pyproject.toml b/pyproject.toml index 68d8eeb..fcec71e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ dependencies = [ "biotite", "gpcrmining", ] -requires-python = "==3.12" +requires-python = "==3.10" [project.urls] Documentation = "https://pensa.readthedocs.io/en/latest/" From c2f4c6699234320f8f206f7720cd6493777c36b7 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:39:25 -0500 Subject: [PATCH 07/15] py 3.10 --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fcec71e..d880e1e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ classifiers = [ "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Physics", @@ -36,7 +37,7 @@ dependencies = [ "biotite", "gpcrmining", ] -requires-python = "==3.10" +requires-python = "3.10" [project.urls] Documentation = "https://pensa.readthedocs.io/en/latest/" From 713911d103036f0b9b0557a27eb9d484e8c5daa6 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:41:05 -0500 Subject: [PATCH 08/15] py 3.10 --- .github/workflows/python-package-conda.yml | 2 +- environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index d982fb5..419fb0d 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -15,7 +15,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v4 with: - python-version: 3.10 + python-version: '3.10' - name: Lint with flake8 run: | pip install flake8 diff --git a/environment.yml b/environment.yml index 1d98214..b6d49a9 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - defaults dependencies: - - python==3.10 + - python=="3.10" - scipy - numpy - pandas From d82ceef113c3fa8bd3b51b81f52a58382b55ec1f Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:42:55 -0500 Subject: [PATCH 09/15] py 3.10 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index b6d49a9..1d98214 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - defaults dependencies: - - python=="3.10" + - python==3.10 - scipy - numpy - pandas From 4c4582b41ce84c76400022f7bccd2c8d0c90df70 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:44:02 -0500 Subject: [PATCH 10/15] py 3.10 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d880e1e..7f1bdd6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "biotite", "gpcrmining", ] -requires-python = "3.10" +requires-python = "==3.10" [project.urls] Documentation = "https://pensa.readthedocs.io/en/latest/" From c1d17c7da6b77b10f4191b0799b173ce69d69c8a Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:45:46 -0500 Subject: [PATCH 11/15] py 3.10 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7f1bdd6..c62db4f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,11 +33,11 @@ dependencies = [ "pandas", "matplotlib", "deeptime", - "MDAnalysis==2.8", + "MDAnalysis=2.8", "biotite", "gpcrmining", ] -requires-python = "==3.10" +requires-python = "=3.10" [project.urls] Documentation = "https://pensa.readthedocs.io/en/latest/" From 612d4380aef23c3a4fc683a1121a6a23d3319c08 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 16:47:44 -0500 Subject: [PATCH 12/15] py 3.10 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c62db4f..7a7dbaa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,11 +33,11 @@ dependencies = [ "pandas", "matplotlib", "deeptime", - "MDAnalysis=2.8", + "MDAnalysis==2.8", "biotite", "gpcrmining", ] -requires-python = "=3.10" +requires-python = "==3.10.*" [project.urls] Documentation = "https://pensa.readthedocs.io/en/latest/" From b3d9da1e495695387bac330ab8456deefdd87a04 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 18:06:24 -0500 Subject: [PATCH 13/15] replace setup.cfg --- LICENSE | 2 +- pyproject.toml | 5 +++++ setup.cfg | 3 --- 3 files changed, 6 insertions(+), 4 deletions(-) delete mode 100644 setup.cfg diff --git a/LICENSE b/LICENSE index 5607977..9d7da3c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2020-2022 Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity +Copyright (c) 2020-2025 Martin Vögele, Neil Thomson, Sang Truong, Jasper McAvity Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/pyproject.toml b/pyproject.toml index 7a7dbaa..789d1d1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,6 +43,10 @@ requires-python = "==3.10.*" Documentation = "https://pensa.readthedocs.io/en/latest/" Source = "http://github.com/drorlab/pensa" +[metadata] +# Include the license file in the wheel. +license_files = ["LICENSE"] + [tool.setuptools.packages.find] include = [ "pensa", @@ -56,3 +60,4 @@ include = [ + diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 3f48337..0000000 --- a/setup.cfg +++ /dev/null @@ -1,3 +0,0 @@ -[metadata] -# Include the license file in the wheel. -license_files = LICENSE From c23807907d6c8bcf327df13510528642e4608bc4 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 21:38:52 -0500 Subject: [PATCH 14/15] update version for docs --- .readthedocs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 0646f07..9966bf6 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,9 +7,9 @@ version: 2 # Set the OS, Python version and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: "3.9" + python: "3.10" # Build documentation in the docs/ directory with Sphinx sphinx: From e0c43a78092907fac7acad3d756f2d0f8a24b760 Mon Sep 17 00:00:00 2001 From: martinvoegele Date: Sun, 26 Jan 2025 21:41:48 -0500 Subject: [PATCH 15/15] remove old test submission script --- run-test.sb | 14 -------------- 1 file changed, 14 deletions(-) delete mode 100644 run-test.sb diff --git a/run-test.sb b/run-test.sb deleted file mode 100644 index 7f4705c..0000000 --- a/run-test.sb +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -#SBATCH --time=24:00:00 -#SBATCH --mem=20G -#SBATCH --partition=rondror -#SBATCH --qos=high_p - -# Activate PENSA environment -source /home/users/mvoegele/miniconda3/etc/profile.d/conda.sh -conda activate /oak/stanford/groups/rondror/users/mvoegele/envs/pensa_dev - -# Run the tests -pytest -