don't use editable installations for ci/cd. revert to setup.py

.github/workflows/github_actions.yml

@@ -50,9 +50,7 @@ jobs:
           openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif 
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
-          pip install -e .
-          pip install -e ColabFold --no-deps
-          pip install -e alphafold --no-deps
+          pip install .
           pip install -U "jax[cuda12]"
           # export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH
           # install dependencies for AlphaLink backend

docker/pulldown.dockerfile

@@ -50,8 +50,6 @@ RUN ssh-keyscan github.com >> /root/.ssh/known_hosts
 RUN --mount=type=ssh git clone --recurse-submodules git@github.com:KosinskiLab/AlphaPulldown.git
 WORKDIR AlphaPulldown
 RUN pip3 install .
-RUN pip3 install -e ColabFold --no-deps
-RUN pip3 install -e alphafold --no-deps
 
 RUN pip3 install --upgrade pip --no-cache-dir \
     && pip3 install --upgrade --no-cache-dir \

pyproject.toml

@@ -1,103 +0,0 @@
-[build-system]
-requires = ["setuptools", "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"
-authors = [
-    { name = "EMBL Hamburg", email = "alphapulldown@embl-hamburg.de" }
-]
-urls = { "Homepage" = "https://github.com/KosinskiLab/AlphaPulldown" }
-classifiers = [
-    'Topic :: Scientific/Engineering :: Artificial Intelligence',
-    'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: Apache Software License',
-    'Operating System :: POSIX :: Linux',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
-    'Programming Language :: Python :: 3.10',
-    'Programming Language :: Python :: 3.11',
-]
-dependencies = [
-    "absl-py >= 0.13.0",
-    "dm-haiku",
-    "dm-tree >= 0.1.6",
-    "h5py >= 3.1.0",
-    "matplotlib >= 3.3.3",
-    "ml-collections >= 0.1.0",
-    "pandas >= 1.5.3",
-    "importlib-resources >= 6.1.0",
-    "biopython >= 1.82",
-    "nbformat >= 5.9.2",
-    "py3Dmol == 2.0.4",
-    "ipython == 8.16.1",
-    "tqdm >= 4.66.1",
-    "appdirs >= 1.4.4",
-    "ml-dtypes",
-    "setuptools >= 40.1.0",
-    "jupyterlab >= 3.0",
-    "ipywidgets",
-    "pytest >= 6.0",
-    "importlib-metadata >= 4.8.2, <5.0.0",
-    "tensorflow-cpu >= 2.16.1",
-    "chex >= 0.1.86",
-    "immutabledict >= 2.0.0"
-]
-dynamic = ["version"]
-
-[tool.setuptools]
-include-package-data = true
-
-[tool.setuptools.package-dir]
-alphafold = "alphafold/alphafold"
-colabfold = "ColabFold/colabfold"
-unifold = "AlphaLink2/unifold"
-
-[tool.setuptools.packages.find]
-where = ["."]
-include = [
-    "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",
-    "colabfold",
-    "analysis_pipeline",
-    "af2plots",
-    "unifold",
-    "unifold.data",
-    "unifold.modules",
-    "unifold.msa",
-    "unifold.losses",
-    "unifold.symmetry"
-]
-
-[tool.setuptools.package-data]
-"alphafold.alphafold.common" = ["stereo_chemical_props.txt"]
-
-[tool.setuptools.dynamic]
-version = { attr = "alphapulldown.__version__" }
-
-[project.scripts]
-"create_individual_features.py" = "alphapulldown.entry_points:create_individual_features"
-"run_multimer_jobs.py" = "alphapulldown.entry_points:run_multimer_jobs"
-"run_structure_prediction.py" = "alphapulldown.entry_points:run_structure_prediction"
-"rename_colab_search_a3m.py" = "alphapulldown.scripts.rename_colab_search_a3m:main"
-"prepare_seq_names.py" = "alphapulldown.scripts.prepare_seq_names:main"
-"generate_crosslink_pickle.py" = "alphapulldown.scripts.generate_crosslink_pickle:main"
-"convert_to_modelcif.py" = "alphapulldown.entry_points:convert_to_modelcif"
-"create_notebook.py" = "alphapulldown.entry_points:create_notebook"
-"get_good_interpae.py" = "alphapulldown.scripts.get_good_interpae:main"
-"truncate_pickle.py" = "alphapulldown.scripts.truncate_pickle:main"

setup.cfg

@@ -0,0 +1,90 @@
+[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
+    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
+    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 
+    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
+    ipython==8.16.1
+    tqdm>=4.66.1
+    appdirs>=1.4.4
+    jupyterlab>=3.0
+    ipywidgets
+    ml-dtypes
+    setuptools>=40.1.0
+    chex>=0.1.86
+    immutabledict>=2.0.0
+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
+
+[options.package_data]
+alphafold.common = stereo_chemical_props.txt

setup.py

@@ -0,0 +1,4 @@
+from setuptools import setup
+from alphapulldown import __version__
+if __name__ == '__main__':
+    setup(version=__version__)