From 5626ba89551f95c33afa229c0409e38eb6da3590 Mon Sep 17 00:00:00 2001 From: Dima Molodenskiy Date: Tue, 3 Feb 2026 20:08:42 +0100 Subject: [PATCH 1/3] New --- pyproject.toml | 114 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..6cccf1c5 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,114 @@ +[build-system] +requires = ["setuptools>=61.0", "wheel"] +build-backend = "setuptools.build_meta" + +[project] +name = "alphapulldown" +description = "Pipeline allows massive screening using alphafold" +readme = { file = "README.md", content-type = "text/markdown" } +requires-python = ">=3.8" +license = "MIT" +license-files = ["LICENSE"] +authors = [ + { name = "EMBL Hamburg", email = "alphapulldown@embl-hamburg.de" } +] +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", +] +dynamic = ["version"] +dependencies = [ + "absl-py>=0.13.0", + "alphapulldown-input-parser>=0.2.0", + "dm-haiku", + "dm-tree>=0.1.6", + "h5py>=3.1.0", + "matplotlib>=3.3.3", + "ml-collections>=0.1.0", + "pandas>=1.5.3", + "tensorflow-cpu>=2.16.1", + "importlib-resources>=6.1.0", + "importlib-metadata>=4.8.2,<5.0.0", + "biopython>=1.82", + "nbformat>=5.9.2", + "py3Dmol==2.0.4", + "pytest>=6.0", + "parameterized", + "ipython==8.16.1", + "tqdm>=4.66.1", + "appdirs>=1.4.4", + "jupyterlab>=3.0", + "ipywidgets", + "ml-dtypes", + "setuptools==70.0.0", + "chex>=0.1.86", + "immutabledict>=2.0.0", + "typing-extensions==4.14.0", +] + +[project.urls] +Homepage = "https://github.com/KosinskiLab/AlphaPulldown" + +[tool.setuptools] +include-package-data = true +packages = [ + "alphapulldown", + "alphapulldown.utils", + "alphapulldown.folding_backend", + "alphapulldown.analysis_pipeline", + "alphapulldown.scripts", + "alphafold", + "alphafold.data", + "alphafold.data.tools", + "alphafold.common", + "alphafold.relax", + "alphafold.model", + "alphafold.model.geometry", + "alphafold.model.tf", + "alphafold.notebooks", + "alphafold3", + "alphafold3.structure", + "colabfold", + "analysis_pipeline", + "af2plots", + "unifold", + "unifold.data", + "unifold.modules", + "unifold.msa", + "unifold.losses", + "unifold.symmetry", +] +script-files = [ + "./alphapulldown/scripts/create_individual_features.py", + "./alphapulldown/scripts/run_multimer_jobs.py", + "./alphapulldown/analysis_pipeline/create_notebook.py", + "./alphapulldown/analysis_pipeline/get_good_inter_pae.py", + "./alphapulldown/scripts/rename_colab_search_a3m.py", + "./alphapulldown/scripts/prepare_seq_names.py", + "./alphapulldown/scripts/generate_crosslink_pickle.py", + "./alphapulldown/scripts/convert_to_modelcif.py", + "./alphapulldown/scripts/run_structure_prediction.py", + "./alphapulldown/scripts/truncate_pickles.py", + "./alphafold/run_alphafold.py", +] + +[tool.setuptools.package-dir] +"" = "." +"alphapulldown" = "./alphapulldown" +"alphapulldown.folding_backend" = "./alphapulldown/folding_backend" +"alphafold" = "./alphafold/alphafold" +"alphafold3" = "./alphafold3/src/alphafold3" +"alphafold3.structure" = "./alphafold3/src/alphafold3/structure" +"colabfold" = "./ColabFold/colabfold" +"analysis_pipeline" = "./alphapulldown/analysis_pipeline" +"af2plots" = "./alphapulldown/analysis_pipeline/af2plots/af2plots" +"unifold" = "./AlphaLink2/unifold/" +"unifold.data" = "./AlphaLink2/unifold/data" +"unifold.losses" = "./AlphaLink2/unifold/losses" +"unifold.symmetry" = "./AlphaLink2/unifold/symmetry" + +[tool.setuptools.package-data] +"alphafold.common" = ["stereo_chemical_props.txt"] + +[tool.setuptools.dynamic] +version = { attr = "alphapulldown.__version__" } From 61d313650984b486bce9570a9449c3f399ec28d5 Mon Sep 17 00:00:00 2001 From: Dima Molodenskiy Date: Tue, 3 Feb 2026 20:12:52 +0100 Subject: [PATCH 2/3] Bump 2.1.6 --- alphapulldown/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/alphapulldown/__init__.py b/alphapulldown/__init__.py index 0b167e61..edc60b35 100755 --- a/alphapulldown/__init__.py +++ b/alphapulldown/__init__.py @@ -1 +1 @@ -__version__ = "2.1.5" +__version__ = "2.1.6" From 814c4bfb50053d62d1cee55498ae68b975615153 Mon Sep 17 00:00:00 2001 From: Dima Date: Tue, 3 Feb 2026 20:19:41 +0100 Subject: [PATCH 3/3] Delete old setup.py and setup.cfg --- setup.cfg | 100 ------------------------------------------------------ setup.py | 4 --- 2 files changed, 104 deletions(-) delete mode 100644 setup.cfg delete mode 100755 setup.py diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index a23e85a1..00000000 --- a/setup.cfg +++ /dev/null @@ -1,100 +0,0 @@ -[metadata] -name = alphapulldown -author = EMBL Hamburg -author_email = alphapulldown@embl-hamburg.de -description = Pipeline allows massive screening using alphafold -url = https://github.com/KosinskiLab/AlphaPulldown -long_description = file: README.md -long_description_content_type = text/markdown -classifiers = - Programming Language :: Python :: 3 - License :: OSI Approved :: MIT License - Operating System :: OS Independent - -[options] -packages= - alphapulldown - alphapulldown.utils - alphapulldown.folding_backend - alphapulldown.analysis_pipeline - alphapulldown.scripts - alphafold - alphafold.data - alphafold.data.tools - alphafold.common - alphafold.relax - alphafold.model - alphafold.model.geometry - alphafold.model.tf - alphafold.notebooks - alphafold3 - alphafold3.structure - colabfold - analysis_pipeline - af2plots - unifold - unifold.data - unifold.modules - unifold.msa - unifold.losses - unifold.symmetry - -package_dir = - alphapulldown = ./alphapulldown - alphapulldown.folding_backend = ./alphapulldown/folding_backend - alphafold = ./alphafold/alphafold - alphafold3 = ./alphafold3/src/alphafold3 - alphafold3.structure = ./alphafold3/src/alphafold3/structure - colabfold = ./ColabFold/colabfold - analysis_pipeline = ./alphapulldown/analysis_pipeline - af2plots = ./alphapulldown/analysis_pipeline/af2plots/af2plots - unifold = ./AlphaLink2/unifold/ - unifold.data = ./AlphaLink2/unifold/data - unifold.losses = ./AlphaLink2/unifold/losses - unifold.symmetry = ./AlphaLink2/unifold/symmetry -include_package_data = True - -python_requires = >=3.8 -install_requires = - absl-py>=0.13.0 - alphapulldown-input-parser>=0.2.0 - dm-haiku - dm-tree>=0.1.6 - h5py>=3.1.0 - matplotlib>=3.3.3 - ml-collections>=0.1.0 - pandas>=1.5.3 - tensorflow-cpu>=2.16.1 - importlib-resources>=6.1.0 - importlib-metadata>=4.8.2, <5.0.0 - biopython>=1.82 - nbformat>=5.9.2 - py3Dmol==2.0.4 - pytest>=6.0 - parameterized - ipython==8.16.1 - tqdm>=4.66.1 - appdirs>=1.4.4 - jupyterlab>=3.0 - ipywidgets - ml-dtypes - setuptools==70.0.0 - chex>=0.1.86 - immutabledict>=2.0.0 - typing-extensions==4.14.0 -# jax[cuda12]==0.5.3 - -scripts = ./alphapulldown/scripts/create_individual_features.py - ./alphapulldown/scripts/run_multimer_jobs.py - ./alphapulldown/analysis_pipeline/create_notebook.py - ./alphapulldown/analysis_pipeline/get_good_inter_pae.py - ./alphapulldown/scripts/rename_colab_search_a3m.py - ./alphapulldown/scripts/prepare_seq_names.py - ./alphapulldown/scripts/generate_crosslink_pickle.py - ./alphapulldown/scripts/convert_to_modelcif.py - ./alphapulldown/scripts/run_structure_prediction.py - ./alphapulldown/scripts/truncate_pickles.py - ./alphafold/run_alphafold.py - -[options.package_data] -alphafold.common = stereo_chemical_props.txt diff --git a/setup.py b/setup.py deleted file mode 100755 index 93c59c0e..00000000 --- a/setup.py +++ /dev/null @@ -1,4 +0,0 @@ -from setuptools import setup -from alphapulldown import __version__ -if __name__ == '__main__': - setup(version=__version__) \ No newline at end of file