Merge pull request #14 from andrewtarzia/lp_changes

Changes made while developing another project- quality of life.

Main changes:
- using Ruff, not Black, so new typing and formatting applied.
- Added some docs (major WIP)
- change `force_field` to `forcefield`.

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: mypy src
-  black:
+  ruff-format:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
@@ -35,7 +35,7 @@ jobs:
           python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
-      - run: black --check .
+      - run: ruff format --check .
   pytest:
     # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
     runs-on: ubuntu-22.04

.gitignore

@@ -131,4 +131,5 @@ dmypy.json
 # Version.
 src/cgexplore/_version.py
 testff_iterations.json
-.vscode
+.vscode
+docs/source/_autosummary

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -W --keep-going
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/_templates/class.rst

@@ -0,0 +1,35 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if not item.startswith('_') and item not in inherited_members %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/module.rst

@@ -0,0 +1,68 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: module.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/cgexplore.rst

@@ -0,0 +1,17 @@
+cgexplore
+=========
+
+
+
+
+Beads
+-----
+
+.. toctree::
+  :maxdepth: 1
+
+  CgBeads <_autosummary/cgexplore.CgBeads>
+
+
+
+This docs are a huge WIP.

docs/source/conf.py

@@ -0,0 +1,45 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+from __future__ import annotations
+
+project = "CGExplore"
+project_copyright = "2023, Andrew Tarzia"
+author = "Andrew Tarzia"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.doctest",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx_copybutton",
+]
+
+autosummary_imported_members = True
+
+autodoc_typehints = "description"
+autodoc_member_order = "groupwise"
+autoclass_content = "class"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}
+
+
+templates_path = ["_templates"]
+exclude_patterns: list[str] = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,49 @@
+.. toctree::
+   :hidden:
+   :caption: CGExplore
+   :maxdepth: 2
+
+   cgexplore <cgexplore>
+
+.. toctree::
+  :hidden:
+  :maxdepth: 2
+  :caption: Modules:
+
+  Modules <modules>
+
+============
+Introduction
+============
+
+| GitHub: https://www.github.com/andrewtarzia/CGExplore
+
+
+:mod:`.CGExplore` is a Python library for doing something...
+
+
+
+
+Installation
+------------
+
+TODO
+
+
+Examples
+--------
+
+TODO
+
+
+Acknowledgements
+----------------
+
+I developed much of this code when working in the Pavan group (https://www.gmpavanlab.com/).
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,9 @@
+Modules
+=======
+
+.. autosummary::
+  :toctree: _autosummary
+  :template: module.rst
+  :recursive:
+
+  cgexplore

first_paper_example/analysis.py

@@ -41,7 +41,7 @@ def analyse_cage(
     conformer,
     name,
     output_dir,
-    force_field,
+    forcefield,
     node_element,
     ligand_element,
     database,
@@ -157,7 +157,7 @@ def analyse_cage(
 
         # This is matched to the existing analysis code. I recommend
         # generalising in the future.
-        ff_targets = force_field.get_targets()
+        ff_targets = forcefield.get_targets()
         if "6P8" in name:
             torsions = "toff"
         else:
@@ -206,8 +206,8 @@ def analyse_cage(
                 elif ("b1", "m1", "b1") in (cp, tuple(reversed(cp))):
                     clangle = at.angle.value_in_unit(openmm.unit.degrees)
 
-        force_field_dict = {
-            "ff_id": force_field.get_identifier(),
+        forcefield_dict = {
+            "ff_id": forcefield.get_identifier(),
             "torsions": torsions,
             "vdws": "von",
             "clbb_bead1": "",
@@ -235,7 +235,7 @@ def analyse_cage(
             "min_b2b_distance": min_b2b_distance,
             "radius_gyration": radius_gyration,
             "max_diameter": max_diameter,
-            "force_field_dict": force_field_dict,
+            "forcefield_dict": forcefield_dict,
         }
         with open(output_file, "w") as f:
             json.dump(res_dict, f, indent=4)
@@ -624,27 +624,27 @@ def data_to_array(json_files, output_dir):
         row["c2bb_name"] = c2bb_name
         row["topology"] = t_str
         row["ff_name"] = ff_name
-        row["torsions"] = res_dict["force_field_dict"]["torsions"]
-        row["vdws"] = res_dict["force_field_dict"]["vdws"]
+        row["torsions"] = res_dict["forcefield_dict"]["torsions"]
+        row["vdws"] = res_dict["forcefield_dict"]["vdws"]
         row["run_number"] = 0
 
         row["cltopo"] = int(clbb_name[0])
         if t_str in cage_topology_options(
             "2p3"
         ) or t_str in cage_topology_options("2p4"):
             cltitle = "3C1" if row["cltopo"] == 3 else "4C1"
-            row["c2r0"] = res_dict["force_field_dict"]["c2r0"]
-            row["c2angle"] = res_dict["force_field_dict"]["c2angle"]
+            row["c2r0"] = res_dict["forcefield_dict"]["c2r0"]
+            row["c2angle"] = res_dict["forcefield_dict"]["c2angle"]
             row["target_bite_angle"] = (row["c2angle"] - 90) * 2
 
         elif t_str in cage_topology_options("3p4"):
             cltitle = "4C1"
-            row["c3r0"] = res_dict["force_field_dict"]["c3r0"]
-            row["c3angle"] = res_dict["force_field_dict"]["c3angle"]
+            row["c3r0"] = res_dict["forcefield_dict"]["c3r0"]
+            row["c3angle"] = res_dict["forcefield_dict"]["c3angle"]
 
         row["cltitle"] = cltitle
-        row["clr0"] = res_dict["force_field_dict"]["clr0"]
-        row["clangle"] = res_dict["force_field_dict"]["clangle"]
+        row["clr0"] = res_dict["forcefield_dict"]["clr0"]
+        row["clangle"] = res_dict["forcefield_dict"]["clangle"]
 
         row["bbpair"] = clbb_name + c2bb_name + ff_name
         row["optimised"] = res_dict["optimised"]