Updating the notebooks (#1470)

* shortening many optimizations. Replacing Boehm with conversion reaction where possible. Thermodynamic more robust.

* Correctly install pyswarms in notebooks1

* renamed "model_conversion_reaction" to "conversion_reaction" according to naming scheme in benchmark models as well

* Revert "renamed "model_conversion_reaction" to "conversion_reaction" according to naming scheme in benchmark models as well"

This reverts commit a1a54f7.

* reverted changes and kept original structure. adjusted amici.ipynb

* changed directory

* changed directory II

* Start out with boehm, for optimization etc change to conversion reaction

* fixed custom_objective_function

* for now: more starts with pyswarms.

* changed julia notebooks ever so slightly.

* Revert changes to julia notebook

* Integrate comments

* Correct PEtab logo now.

* Update doc/example/getting_started.ipynb

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

* Update doc/example/getting_started.ipynb

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

* Adjusted amici logo

* Removed pyswarms from waterfall visualization

* Fixed a random seed for sampling notebook

---------

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

doc/example/censored_data.ipynb

@@ -237,7 +237,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "dev_venv",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -251,7 +251,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.3"
   },
   "vscode": {
    "interpreter": {
@@ -260,5 +260,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

doc/example/conversion_reaction.ipynb

@@ -144,6 +144,7 @@
    },
    "outputs": [],
    "source": [
+    "%%time\n",
     "# create objective function from amici model\n",
     "# pesto.AmiciObjective is derived from pesto.Objective,\n",
     "# the general pesto objective function class\n",
@@ -157,7 +158,7 @@
     "\n",
     "# do the optimization\n",
     "result = optimize.minimize(\n",
-    "    problem=problem, optimizer=optimizer, n_starts=100, filename=None\n",
+    "    problem=problem, optimizer=optimizer, n_starts=10, filename=None\n",
     ")"
    ]
   },
@@ -221,7 +222,7 @@
     "    problem=problem,\n",
     "    result=result,\n",
     "    optimizer=optimizer,\n",
-    "    profile_index=np.array([1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0]),\n",
+    "    profile_index=np.array([0,1]),\n",
     "    result_index=0,\n",
     "    profile_options=profile_options,\n",
     "    filename=None,\n",
@@ -270,7 +271,7 @@
     ")\n",
     "\n",
     "result = sample.sample(\n",
-    "    problem, n_samples=10000, sampler=sampler, result=result, filename=None\n",
+    "    problem, n_samples=1000, sampler=sampler, result=result, filename=None\n",
     ")"
    ]
   },
@@ -425,7 +426,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,