CI: basic env

devtools/test_env.yml

@@ -3,72 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.8
-  - pip
-  - jupyterlab>=3
-  # Workaround for jupyterlab, see https://github.com/volkamerlab/teachopencadd/issues/310
-  - jsonschema>=4.3.0
-  - nglview>=3
-  # Workaround for nglview, see https://github.com/volkamerlab/teachopencadd/issues/262
-  - ipywidgets<=7.75
-  - jupyter_client<=7.4.9
-  # New numpy version 1.2.4 too young, e.g. caused
-  # https://github.com/volkamerlab/teachopencadd/issues/299
-  - numpy<1.24
-  - scikit-learn
-  # API changed after v2.6, see https://github.com/volkamerlab/teachopencadd/issues/265
-  - tensorflow<=2.6
-  - seaborn
-  - matplotlib-venn
-  - bravado
-  - requests
-  - requests-cache
-  - redo
-  - suds-community
-  - beautifulsoup4
-  - chembl_webresource_client
-  - pypdb
-  - biopython<=1.77
-  - biopandas
-  - rdkit
-  - openbabel
-  - opencadd
-  - biotite>=0.34.0
-  - smina
-  - mdanalysis>=1.0.0
-  - mdtraj
-  - plip
-  - openmm
-  - mkl < 2022
-  - pytorch::pytorch==1.13.0
-  #- pyg::pyg==2.2.0  # installed manually for now
-  # Dependency not included, see https://github.com/volkamerlab/teachopencadd/issues/313
-  # - openmmforcefields
-  - pdbfixer
-  - tqdm
-  - lxml
-  - kissim
-  ## CI tests
-  - pytest
-  - pytest-xdist
-  - pytest-cov
-  - nbval
-  - shyaml
-  # Workaround for https://github.com/sphinx-doc/sphinx/issues/10289
-  - jinja2==3.0.3
-  ## Docs
-  - sphinx
-  - sphinx-material
-  - nbsphinx
-  - recommonmark
-  - sphinx-autodoc-typehints
-  - sphinx-copybutton
-  - sphinx-gallery
-  - autodocsumm
-  - pip:
-      - black-nb
-      - nbsphinx-link
-      - sphinxext-opengraph
-      - deepchem
-      # TeachOpenCADD itself
-      - ../
+  - python
+  - pyyaml
+  - mamba