diff --git a/.binder/apt.txt b/.binder/apt.txt new file mode 100644 index 0000000..52f9a7b --- /dev/null +++ b/.binder/apt.txt @@ -0,0 +1 @@ +libgl1 \ No newline at end of file diff --git a/.binder/environment.yml b/.binder/environment.yml index 183ffa6..32ca728 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -1,24 +1,26 @@ -channels: - - conda-forge - - defaults -dependencies: - - python=3.9.19 # 3.10 or above provokes numba import fail - - mdanalysis=2.2.0 # 2.3 or above fails with non-complying "formalcharges" last column of PDBs (GPCRmd PDBs) - - numpy=1.23.5 # 1.24 removed numpy.int and numpy.float needed for dynetan and PyInteraph2 - - ipywidgets=7.8.0 # 8 or above messes with nglview - - jupyterlab=3.6.7 # 4 or above messes with nglview - - multiprocess - - lazyasd - - pandas - - pyarrow - - numba - - networkx - - pymol-open-source - - ambertools - - nglview - - prody - - mdtraj - - python-louvain - - compilers - - cython +name: AlloViz +channels: + - conda-forge + - defaults + - conda-forge/label/broken +dependencies: + - python==3.9.* # 3.10 or above provokes numba import fail + - mdanalysis==2.2.* # 2.3 or above fails with non-complying "formalcharges" last column of PDBs (GPCRmd PDBs) + - numpy==1.23.* # 1.24 removed numpy.int and numpy.float needed for dynetan and PyInteraph2 + - ipywidgets==7.* # 8 or above messes with nglview + - jupyterlab==3.* # 4 or above messes with nglview + - multiprocess + - lazyasd + - pandas + - pyarrow + - numba + - networkx + - pymol-open-source + - ambertools + - nglview + - prody + - mdtraj + - python-louvain + - compilers + - cython - vmd-python \ No newline at end of file diff --git a/.readthedocs.yaml b/.readthedocs.yaml index d4a4f73..0cc1a66 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ build: python: "3.10" jobs: pre_install: - - sed -i "s/dependencies = .*//g" pyproject.toml + - sed -i '/dependencies = .*/,+25d' pyproject.toml sphinx: fail_on_warning: false diff --git a/pyproject.toml b/pyproject.toml index 8c319c4..8ddcf9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,11 +18,10 @@ readme = "README.rst" version = "1.0" dependencies = [ - # removed loose version specifications; messes with readthedocs - 'numpy', # <1.24 # 1.24 removed numpy.int and numpy.float needed for dynetan and PyInteraph2 - 'ipywidgets', # <8 # 8 or above messes with nglview - 'jupyterlab', # <4 # 4 or above messes with nglview - 'mdanalysis', # >=2.2,<2.3 # 2.3 or above fails with non-complying "formalcharges" last column of PDBs (GPCRmd PDBs) + 'numpy < 1.24', # 1.24 removed numpy.int and numpy.float needed for dynetan and PyInteraph2 + 'ipywidgets < 8', # 8 or above messes with nglview + 'jupyterlab < 4', # 4 or above messes with nglview + 'mdanalysis >= 2.2, < 2.3', # 2.3 or above fails with non-complying "formalcharges" last column of PDBs (GPCRmd PDBs) 'multiprocess', 'lazyasd', @@ -43,6 +42,14 @@ dependencies = [ 'vmd-python' ] + + + + + + + + # license = {text = "BSD 3-Clause License"} classifiers = [ # "License :: OSI Approved :: MIT License",