Bump versions and switch to uv

.github/workflows/ci.yml

@@ -39,13 +39,13 @@ jobs:
         include:
           - label: earliest
             os: ubuntu-latest
-            python-version: 3.8
-            rdkit-version: "rdkit=2021.03.1"
+            python-version: 3.9
+            rdkit-version: "rdkit==2022.09.1"
             coverage: false
           - label: baseline
             os: ubuntu-latest
             python-version: "3.10"
-            rdkit-version: "rdkit~=2022.09"
+            rdkit-version: "rdkit~=2023.03.1"
             coverage: true
           - label: latest
             os: ubuntu-latest
@@ -58,14 +58,10 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
           auto-update-conda: true
-          channel-priority: flexible
-          channels: conda-forge, defaults
-          add-pip-as-python-dependency: true
-          architecture: x64
           use-mamba: true
           miniforge-variant: Mambaforge
 
@@ -79,13 +75,13 @@ jobs:
 
       - name: Install conda dependencies
         run: |
-          mamba install ${{ matrix.rdkit-version }}
+          mamba install uv ${{ matrix.rdkit-version }}
           mamba list
 
       - name: Install package through pip
         run: |
-          pip install .[dev]
-          pip list
+          uv pip install .[dev]
+          uv pip list
 
       - name: Run tests
         run: |

.github/workflows/formatting.yml → .github/workflows/formatting_linting.yml

@@ -1,4 +1,4 @@
-name: "Black"
+name: "Ruff/Black"
 
 on:
   push:
@@ -19,6 +19,12 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Code formatting
+        uses: chartboost/ruff-action@v1
+        with:
+          args: "check --preview"
+
+      - name: Notebook formatting
         uses: psf/black@stable
         with:
+          src: "docs/notebooks/"
           jupyter: true

.readthedocs.yml

@@ -1,13 +1,15 @@
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: mambaforge-4.10
+    python: mambaforge-22.9
 sphinx:
   configuration: docs/conf.py
 python:
   install:
-  - method: pip
-    path: .
+    - method: pip
+      path: .
+      extra_requirements:
+        - tutorials
 conda:
   environment: environment.yml

CHANGELOG.md

@@ -6,6 +6,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- `Complex3D` and `fp.plot_3d` now have access to `only_interacting` and
+  `remove_hydrogens` parameters to control which residues and hydrogen atoms are
+  displayed. Non-polar hydrogen atoms that aren't involved in interactions are now
+  hidden by default.
+- `LigNetwork.save_png` to save the displayed plot to a PNG file through JavaScript
+  (Issue #163).
+- `Complex3D.save_png` to save the displayed plot to a PNG file through JavaScript.
+- `fp.plot_3d` and `fp.plot_lignetwork` now return the underlying `LigNetwork` or
+  `Complex3D` object which has been enhanced with rich display functionality. From the
+  user's perspective, nothing changes apart from being able to do
+  `view = fp.plot_*(...); view.save_png()` to display a popup window for saving the
+  image.
+- `cleanup_substructures` parameter now accessible in `mol2_supplier` to skip
+  sanitization based on atom types.
+- `sanitize` parameter now available for the `mol2_supplier` and `sdf_supplier` classes.
+- `ruff` linter and formatter.
+
+### Fixed
+
+- `display_residues` was sanitizing each residue while preparing them for display, which
+  could make debugging faulty molecules difficult. This is now disabled.
+- Deprecation warnings
+
 ## [2.0.3] - 2024-03-10
 
 ### Fixed

docs/conf.py

@@ -10,6 +10,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+# ruff: noqa: PTH100
 import os
 import sys
 
@@ -24,7 +25,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "ProLIF"
-copyright = f"2017-{datetime.now().year}, Cédric Bouysset"
+copyright = f"2017-{datetime.now().year}, Cédric Bouysset"  # noqa: A001
 author = "Cédric Bouysset"
 
 
@@ -99,7 +100,7 @@
             "url": "https://github.com/chemosim-lab/ProLIF",
             "icon": "fa-brands fa-square-github",
             "type": "fontawesome",
-        }
+        },
     ],
 }
 
@@ -123,7 +124,7 @@ def setup(app):
     app.add_config_value(
         "recommonmark_config",
         {
-            #'url_resolver': lambda url: github_doc_root + url,
+            # 'url_resolver': lambda url: github_doc_root + url,
             "auto_toc_tree_section": "Contents",
             "enable_math": False,
             "enable_inline_math": False,

docs/notebooks/docking.ipynb

@@ -699,7 +699,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fp.plot_lignetwork(pose_iterable[0])"
+    "view = fp.plot_lignetwork(pose_iterable[0])\n",
+    "view"
    ]
   },
   {
@@ -713,7 +714,11 @@
     "- hover an interaction line to display the distance.\n",
     "\n",
     ":::{note}\n",
-    "It is not possible to export it as an image, but you can always take a screenshot.\n",
+    "After arranging the residues to your liking, you can save the plot as a PNG image with:\n",
+    "```python\n",
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts.\n",
     ":::\n",
     "\n",
     "You can generate 2 types of diagram with this function, controlled by the `kind` argument:\n",
@@ -735,7 +740,8 @@
    "outputs": [],
    "source": [
     "pose_index = 0\n",
-    "fp.plot_lignetwork(pose_iterable[pose_index], kind=\"frame\", frame=pose_index)"
+    "view = fp.plot_lignetwork(pose_iterable[pose_index], kind=\"frame\", frame=pose_index)\n",
+    "view"
    ]
   },
   {
@@ -753,9 +759,10 @@
    "source": [
     "fp_count = plf.Fingerprint(count=True)\n",
     "fp_count.run_from_iterable(pose_iterable, protein_mol)\n",
-    "fp_count.plot_lignetwork(\n",
+    "view = fp_count.plot_lignetwork(\n",
     "    pose_iterable[pose_index], kind=\"frame\", frame=pose_index, display_all=True\n",
-    ")"
+    ")\n",
+    "view"
    ]
   },
   {
@@ -785,22 +792,12 @@
     "\n",
     "The advantage of using a count fingerprint in that case is that it will automatically select the interaction occurence with the shortest distance for a more intuitive visualization.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with:\n",
     "\n",
     "```python\n",
-    "from IPython.display import Javascript\n",
-    "\n",
-    "Javascript(\n",
-    "    \"\"\"\n",
-    "    var png = viewer_%s.pngURI()\n",
-    "    var a = document.createElement('a')\n",
-    "    a.href = png\n",
-    "    a.download = \"prolif-3d.png\"\n",
-    "    a.click()\n",
-    "    a.remove()\n",
-    "    \"\"\"\n",
-    "    % view.uniqueid\n",
-    ")\n",
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts.\n",
     "```"
    ]
   },

docs/notebooks/md-ligand-protein.ipynb

@@ -550,7 +550,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fp.plot_lignetwork(ligand_mol)"
+    "view = fp.plot_lignetwork(ligand_mol)\n",
+    "view"
    ]
   },
   {
@@ -564,7 +565,11 @@
     "- hover an interaction line to display the distance.\n",
     "\n",
     ":::{note}\n",
-    "It is not possible to export it as an image, but you can always take a screenshot.\n",
+    "After arranging the residues to your liking, you can save the plot as a PNG image with:\n",
+    "```python\n",
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts.\n",
     ":::\n",
     "\n",
     "You can generate 2 types of diagram with this function, controlled by the `kind` argument:\n",
@@ -585,7 +590,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fp.plot_lignetwork(ligand_mol, threshold=0.0)"
+    "view = fp.plot_lignetwork(ligand_mol, threshold=0.0)\n",
+    "view"
    ]
   },
   {
@@ -603,7 +609,8 @@
    "source": [
     "fp_count = plf.Fingerprint(count=True)\n",
     "fp_count.run(u.trajectory[0:1], ligand_selection, protein_selection)\n",
-    "fp_count.plot_lignetwork(ligand_mol, kind=\"frame\", frame=0, display_all=True)"
+    "view = fp_count.plot_lignetwork(ligand_mol, kind=\"frame\", frame=0, display_all=True)\n",
+    "view"
    ]
   },
   {
@@ -637,23 +644,12 @@
     "\n",
     "The advantage of using a count fingerprint in that case is that it will automatically select the interaction occurence with the shortest distance for a more intuitive visualization.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with:\n",
     "\n",
     "```python\n",
-    "from IPython.display import Javascript\n",
-    "\n",
-    "Javascript(\n",
-    "    \"\"\"\n",
-    "    var png = viewer_%s.pngURI()\n",
-    "    var a = document.createElement('a')\n",
-    "    a.href = png\n",
-    "    a.download = \"prolif-3d.png\"\n",
-    "    a.click()\n",
-    "    a.remove()\n",
-    "    \"\"\"\n",
-    "    % view.uniqueid\n",
-    ")\n",
-    "```"
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts."
    ]
   },
   {
@@ -708,7 +704,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

docs/notebooks/md-protein-protein.ipynb

@@ -578,7 +578,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fp.plot_lignetwork(small_protein_mol)"
+    "view = fp.plot_lignetwork(small_protein_mol)\n",
+    "view"
    ]
   },
   {
@@ -592,7 +593,11 @@
     "- hover an interaction line to display the distance.\n",
     "\n",
     ":::{note}\n",
-    "It is not possible to export it as an image, but you can always take a screenshot.\n",
+    "After arranging the residues to your liking, you can save the plot as a PNG image with:\n",
+    "```python\n",
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts.\n",
     ":::\n",
     "\n",
     "You can generate 2 types of diagram with this function, controlled by the `kind` argument:\n",
@@ -647,23 +652,12 @@
    "source": [
     "As in the lignetwork plot, you can hover atoms and interactions to display more information.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with:\n",
     "\n",
     "```python\n",
-    "from IPython.display import Javascript\n",
-    "\n",
-    "Javascript(\n",
-    "    \"\"\"\n",
-    "    var png = viewer_%s.pngURI()\n",
-    "    var a = document.createElement('a')\n",
-    "    a.href = png\n",
-    "    a.download = \"prolif-3d.png\"\n",
-    "    a.click()\n",
-    "    a.remove()\n",
-    "    \"\"\"\n",
-    "    % view.uniqueid\n",
-    ")\n",
-    "```"
+    "view.save_png()\n",
+    "```\n",
+    "Note that this only works in notebooks and cannot be used in regular Python scripts."
    ]
   },
   {