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klamt-lab · Jun 9, 2022 · 36746b2 · 36746b2
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diff --git a/docs/source/examples/JN_03_plotting.ipynb b/docs/source/examples/JN_03_plotting.ipynb
diff --git a/docs/source/examples/JN_04_strain_design_introduction.ipynb b/docs/source/examples/JN_04_strain_design_introduction.ipynb
@@ -7,6 +7,13 @@
  "# Computational strain design: Growth-coupling principles"
  ]
  },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Continued.."
+ ]
+ },
  {
  "cell_type": "markdown",
  "metadata": {},

diff --git a/docs/source/examples/JN_05_strain_design_mcs.ipynb b/docs/source/examples/JN_05_strain_design_mcs.ipynb
@@ -16,32 +16,68 @@
  },
  {
  "cell_type": "code",
- "execution_count": 14,
+ "execution_count": 5,
  "metadata": {},
  "outputs": [
  {
- "ename": "TypeError",
- "evalue": "'SDSolution' object is not iterable",
- "output_type": "error",
- "traceback": [
- "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)",
- "\u001b[1;32mc:\\Users\\Philipp\\Documents\\Python\\straindesign\\docs\\source\\examples\\JN_05_strain_design_mcs.ipynb Cell 3'\u001b[0m in \u001b[0;36m<cell line: 9>\u001b[1;34m()\u001b[0m\n\u001b[0;32m <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_05_strain_design_mcs.ipynb#ch0000004?line=5'>6</a>\u001b[0m modules \u001b[39m+\u001b[39m\u001b[39m=\u001b[39m [sd\u001b[39m.\u001b[39mSDModule(model,sd\u001b[39m.\u001b[39mnames\u001b[39m.\u001b[39mSUPPRESS,constraints\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mR4 <= 1\u001b[39m\u001b[39m'\u001b[39m)]\n\u001b[0;32m <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_05_strain_design_mcs.ipynb#ch0000004?line=7'>8</a>\u001b[0m sols \u001b[39m=\u001b[39m sd\u001b[39m.\u001b[39mcompute_strain_designs(model,sd_modules \u001b[39m=\u001b[39m modules)\n\u001b[1;32m----> <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_05_strain_design_mcs.ipynb#ch0000004?line=8'>9</a>\u001b[0m \u001b[39mfor\u001b[39;00m s \u001b[39min\u001b[39;00m sols:\n\u001b[0;32m <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_05_strain_design_mcs.ipynb#ch0000004?line=9'>10</a>\u001b[0m \u001b[39mprint\u001b[39m(s\u001b[39m.\u001b[39msd_solutions)\n",
- "\u001b[1;31mTypeError\u001b[0m: 'SDSolution' object is not iterable"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+  "{'R1': -1.0}\n",
+ "{'R4': -1.0}\n",
+ "{'R7': -1.0}\n",
+ "{'R10': -1.0}\n",
+ "{'R6': -1.0, 'R8': -1.0}\n"
  ]
  }
  ],
  "source": [
  "import straindesign as sd\n",
  "import cobra\n",
+ "\n",
  "model = cobra.io.read_sbml_model('../../../tests/model_small_example.xml')\n",
  "\n",
  "modules = [sd.SDModule(model,sd.names.PROTECT, constraints='R3 >= 1')]\n",
- "modules += [sd.SDModule(model,sd.names.SUPPRESS,constraints='R4 <= 1')]\n",
+ "modules += [sd.SDModule(model,sd.names.SUPPRESS,constraints='R4 >= 1')]\n",
  "\n",
  "sols = sd.compute_strain_designs(model,sd_modules = modules)\n",
- "for s in sols:\n",
- " print(s.sd_solutions)"
+ "for s in sols.reaction_sd:\n",
+ " print(s)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "To see the current status of the strain design computation, import the logging package and lower the reporting level."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[]"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "import logging\n",
+ "logging.basicConfig(level=logging.INFO)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Continued.."
  ]
  },
  {

diff --git a/docs/source/examples/JN_06_strain_design_nested.ipynb b/docs/source/examples/JN_06_strain_design_nested.ipynb
@@ -7,6 +7,13 @@
  "# Multi-level strain optimization approaches"
  ]
  },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Continued ..."
+ ]
+ },
  {
  "cell_type": "markdown",
  "metadata": {},

diff --git a/docs/source/examples/JN_07_network_design.ipynb b/docs/source/examples/JN_07_network_design.ipynb
@@ -7,6 +7,13 @@
  "# Tailoring metabolic networks"
  ]
  },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Continued .."
+ ]
+ },
  {
  "cell_type": "markdown",
  "metadata": {},

diff --git a/docs/source/examples/JN_08_compression.ipynb b/docs/source/examples/JN_08_compression.ipynb
@@ -7,6 +7,13 @@
  "# Network Compression\n"
  ]
  },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Continued .."
+ ]
+ },
  {
  "cell_type": "markdown",
  "metadata": {},

diff --git a/straindesign/compute_strain_designs.py b/straindesign/compute_strain_designs.py
@@ -38,6 +38,8 @@ def compute_strain_designs(model: Model, **kwargs):
 
  if MAX_COST in kwargs:
  kwargs.update({MAX_COST: float(kwargs.pop(MAX_COST))})
+ else:
+ kwargs.update({MAX_COST: np.inf})
 
  if MODEL_ID in kwargs:
  model_id = kwargs.pop(MODEL_ID)