Merge pull request PolusAI#209 from jfennick/move_mm_viewer

move molecular modeling viewer
jfennick · Apr 11, 2024 · 3f3912a · 3f3912a
2 parents e6f59d6 + c6502e4
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diff --git a/README.md b/README.md
@@ -75,18 +75,6 @@ timeseriesplots
 
 ![Plots](examples/gromacs/plots.png)
 
-You can also view the 3D structures in the Jupyter notebook `src/vis/viewer.ipynb`. The visualization currently needs to be in its own conda environment.
-
-```
-install/install_conda.sh
-conda create --name vis
-conda activate vis
-install/install_nglview.sh
-pip install -e ".[all]"
-```
-
-![Plots](docs/tree_viewer.png)
-
 The Workflow Inference Compiler is a [Domain Specific Language](https://en.wikipedia.org/wiki/Domain-specific_language) (DSL) based on the [Common Workflow Language](https://www.commonwl.org). CWL is fantastic, but explicitly constructing the Directed Acyclic Graph (DAG) associated with a non-trivial workflow is not so simple. For example, the workflow shown above is based on the following [gromacs tutorial](https://mmb.irbbarcelona.org/biobb/availability/tutorials/cwl). Instead of writing raw CWL, you can write your workflows in a much simpler yml DSL. For technical reasons edge inference is far from unique, so ***`users should always check that edge inference actually produces the intended DAG`***.
 
 ## Edge Inference

diff --git a/docs/dev/api.rst b/docs/dev/api.rst
@@ -1,14 +1,6 @@
 Developer API
 ====================================
 
-vis.filewatcher
-------------------------------------
-.. automodule:: vis.filewatcher
-
-vis.viewer
-------------------------------------
-.. automodule:: vis.viewer
-
 wic.ast
 ------------------------------------
 .. automodule:: wic.ast

diff --git a/docs/installguide.md b/docs/installguide.md
@@ -89,18 +89,6 @@ pre-commit install
 
 You should now have the `wic` executable available in your terminal.
 
-## Jupyter notebook visualization
-
-The visualization currently needs to be in its own conda environment.
-
-```
-./install_conda.sh
-conda create --name vis
-conda activate vis
-./install_nglview.sh
-pip install -e ".[all]"
-```
-
 ## CUDA
 
 Some of the workflows require an Nvidia CUDA GPU. Please see the Nvidia [installation guides](https://docs.nvidia.com/cuda/#installation-guides) for more information.

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,3 @@
-ipytree
 myst-parser
 # https://docs.readthedocs.io/en/stable/intro/getting-started-with-sphinx.html
 # "We strongly recommend to pin the Sphinx version used for your project to build the docs to avoid potential future incompatibilities."

diff --git a/docs/tree_viewer.png b/docs/tree_viewer.png
diff --git a/docs/tutorials/multistep.md b/docs/tutorials/multistep.md
@@ -54,12 +54,6 @@ docs/tutorials/multistep1.yml.gv.png
 
 The first thing you might notice is the `!&` and `!*` notation. This is the syntax for explicitly creating an edge between an output and a later input. Note that `!&` must come first and can only be defined once, but then you can use `!*` multiple times in any later step.
 
-## Visualizing the results
-
-This particular workflow creates files which represent 3D coordinates, so we can view them in the Jupyter notebook `src/vis/viewer.ipynb`. Make sure you are using the `vis` conda environment as mentioned in the installation guide.
-
-![Multistep](protein.png)
-
 ## Edge Inference
 
 Creating explicit edges can be a bit tedious and verbose, but in many cases the correct edges can be determined automatically. In this case, all of the steps take the previous pdb file as input and produce an output pdb file, so this is rather trivial. However, for more complex workflows edge inference can drastically simplify the yml files. Note that explicit edges are drawn in blue, and inferred edges are drawn in black/white.

diff --git a/docs/tutorials/protein.png b/docs/tutorials/protein.png
diff --git a/install/install_nglview.sh b/install/install_nglview.sh
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,6 @@
 # Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/
 [build-system]
 requires = ["setuptools>=42,<68", "wheel", "versioneer[toml]==0.29"]
-# NOTE: The above list mostly comes from https://github.com/nglviewer/nglview/pull/969/files
 # NOTE: Use upper bound of <68 for setuptools due to 2to3 error.
 # See https://stackoverflow.com/questions/72414481/error-in-anyjson-setup-command-use-2to3-is-invalid
 
@@ -30,7 +29,6 @@ dependencies = [
     "requests",
     "mergedeep",
     "networkx",
-    "beautifulsoup4", # Solely for parsing gromacs mdp options html
     "cwl-utils>=0.32",
     # CommandInputParameter attr changed from `type_` to `type` and back to `type_`
     # between versions 0.30, 0.31, 0.32
@@ -109,7 +107,6 @@ doc = [
     "sphinx",
     "myst-parser",
     "sphinx-autodoc-typehints",
-    "ipytree",
 ]
 plots = ["matplotlib"]
 cyto = ["ipycytoscape"] # only for DAG visualization
@@ -211,10 +208,7 @@ module = [
     "graphviz.*",
     "mergedeep.*",
     "networkx.*",
-    "mdtraj.*",
-    "nglview.*",
     "matplotlib.*",
-    "ipytree.*",
     "ipywidgets.*",
     "scipy.*",
     "ruamel.*",

diff --git a/src/vis/__init__.py b/src/vis/__init__.py
diff --git a/src/vis/filewatcher.py b/src/vis/filewatcher.py
diff --git a/src/vis/viewer.ipynb b/src/vis/viewer.ipynb