Update to Python=3.9 and update Django

.gitignore

@@ -44,9 +44,6 @@ rmgweb/media/rmg/tools/*
 .pydevproject
 .settings/*
 
-# WSGI
-apache/django.wsgi
-
 # VS Code related files
 .history/*
 

environment.yml

@@ -1,19 +1,19 @@
 # First, install a conda environment with RMG-Py.
 # Then, update the environment using the constraints in this environment file.
 
-name: rmg_env
+name: rmg_website
 channels:
-  - rmg
   - conda-forge
-  - cantera
+  - simonabuzzi
   - fhvermei
 dependencies:
-  - docutils
-  - django =2.2
-  - lxml
+  - django==4.2
   - pip
   - pip:
-      - git+https://github.com/bp-kelley/[email protected]
-  - python >=3.7
-  - solprop_ml >=1.2
+      - git+https://github.com/bp-kelley/descriptastorus
+  - simonabuzzi::solprop_ml_mix
+  - wandb # Required for solprop_ml_mix
+  - python>=3.9
   - xlsxwriter
+  - fhvermei::chemprop_solvation
+  - cantera==2.6.0*

rmgweb/database/templates/kineticsTable.html

@@ -78,11 +78,11 @@
 var treeChildren = new Array();
 
 {% for entry in entries %}
-    {% ifequal entry.parent None %}
+    {% if entry.parent == None %}
     treeParent["{{ entry.index }}"] = "";
     {% else %}
     treeParent["{{ entry.index }}"] = "{{ entry.parent.index }}";
-    {% endifequal %}
+    {% endif %}
     treeChildren["{{ entry.index }}"] = [{% for child in entry.children %}"{{ child.index }}"{% if not forloop.last %}, {% endif %}{% endfor %}];
 {% endfor %}
 

rmgweb/database/templates/thermoEntry.html

@@ -89,7 +89,7 @@ <h2>Structure</h2>
 </p>
 
 <h2>Thermodynamic Data</h2>
-{% ifequal thermo.0 'Link' %}
+{% if thermo.0 == 'Link' %}
 <table class="thermoEntryData">
 <tr>
     <td class="key">Link:</td>
@@ -98,7 +98,7 @@ <h2>Thermodynamic Data</h2>
 </table>
 {% else %}
 {{ thermo|render_thermo_math:user }}
-{% endifequal %}
+{% endif %}
 
 {% if nasa_string %}
 <br/>

rmgweb/database/tools.py

@@ -390,7 +390,6 @@ def generateReactions(database, reactants, products=None, only_families=None, re
         reactants, products, only_families=only_families, resonance=resonance)
     if len(reactants) == 1:
         # if only one reactant, react it with itself bimolecularly, with RMG-py
-        # the java version already does this (it includes A+A reactions when you react A)
         reactants2 = [reactants[0], reactants[0]]
         reaction_list.extend(database.kinetics.generate_reactions(
             reactants2, products, only_families=only_families, resonance=resonance))

rmgweb/main/migrations/0002_alter_userprofile_id.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.23 on 2025-07-03 15:10
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("main", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="userprofile",
+            name="id",
+            field=models.BigAutoField(
+                auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+            ),
+        ),
+    ]

rmgweb/main/templatetags/render_solvation.py

@@ -37,7 +37,7 @@
 from rmgpy.data.base import Entry
 from rmgpy.species import Species
 from rmgpy.molecule.group import Group
-from rmgpy.data.solvation import *
+from rmgpy.data.solvation import SoluteData, SolventData, SolvationCorrection
 
 # Register this module as a Django template tag library
 register = template.Library()

rmgweb/main/views.py

@@ -44,6 +44,9 @@
 from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 
+from rmgpy.molecule.group import Group
+from rmgpy.molecule.adjlist import InvalidAdjacencyListError
+
 from rmgpy.molecule.atomtype import allElements as SUPPORTED_ELEMENTS
 
 from rmgweb.main.forms import *
@@ -68,6 +71,10 @@
     elif len(element) == 2:
         SUPPORTED_ELEMENTS_TWO_LETTERS.append(element)
 
+# add conda environment bin to PATH. Added on 3 July 2025 to ensure graphviz is added to path, even if bashrc is not sourced.
+bin = os.path.join(os.environ.get("CONDA_PREFIX", ""), "bin")
+if bin and bin not in os.environ["PATH"]:
+    os.environ["PATH"] = bin + os.pathsep + os.environ["PATH"]
 
 def index(request):
     """
@@ -354,30 +361,28 @@ def drawGroup(request, adjlist, format='png'):
     Returns an image of the provided adjacency list `adjlist` for a molecular
     group.  urllib is used to quote/unquote the adjacency list.
     """
-    from rmgpy.molecule.group import Group
-    from rmgpy.molecule.adjlist import InvalidAdjacencyListError
 
     adjlist = urllib.parse.unquote(adjlist)
 
-    # try:
-    #     group = Group().from_adjacency_list(adjlist)
-    # except (InvalidAdjacencyListError, ValueError):
-    #     response = HttpResponseRedirect(static('img/invalid_icon.png'))
-    # else:
-    #     if format == 'png':
-    #         response = HttpResponse(content_type="image/png")
-    #         response.write(group.draw('png'))
-    #     elif format == 'svg':
-    #         response = HttpResponse(content_type="image/svg+xml")
-    #         svg_data = group.draw('svg')
-    #         # Remove the scale and rotate transformations applied by pydot
-    #         svg_data = re.sub(r'scale\(0\.722222 0\.722222\) rotate\(0\) ', '', svg_data)
-    #         response.write(svg_data)
-    #     else:
-    #         response = HttpResponse('Image format not implemented.', status=501)
-
-    # return response
-    return HttpResponse(content_type="image/png") # TODO: fix root cause. Added 3/31/25 as a stopgap to prevent 'neato not found' errors.
+    try:
+        group = Group().from_adjacency_list(adjlist)
+    except (InvalidAdjacencyListError, ValueError):
+        response = HttpResponseRedirect(static('img/invalid_icon.png'))
+    else:
+        if format == 'png':
+            response = HttpResponse(content_type="image/png")
+            response.write(group.draw('png'))
+        elif format == 'svg':
+            response = HttpResponse(content_type="image/svg+xml")
+            svg_data = group.draw('svg')
+            # Remove the scale and rotate transformations applied by pydot
+            svg_data = re.sub(r'scale\(0\.722222 0\.722222\) rotate\(0\) ', '', svg_data)
+            response.write(svg_data)
+        else:
+            response = HttpResponse('Image format not implemented.', status=501)
+
+    return response
+#    return HttpResponse(content_type="image/svg+xml")
 
 
 @login_required

rmgweb/pdep/models.py

@@ -72,7 +72,8 @@ def getDirname(self):
         Return the absolute path of the directory that the Network object uses
         to store files.
         """
-        return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', str(self.pk))
+        pk_str = self.pk.decode() if isinstance(self.pk, bytes) else str(self.pk)
+        return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', pk_str)
 
     def getInputFilename(self):
         """