feat: expanded and added tutorials

biosimulators · Oct 7, 2021 · 62b6141 · 62b6141
1 parent 84299c9
commit 62b6141
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Showing 21 changed files with 46,722 additions and 140 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -9,7 +9,7 @@ biosimulators-cbmpy
 biosimulators-copasi
 biosimulators-cobrapy
 biosimulators-tellurium
-biosimulators-utils[sbml,logging,containers]
+biosimulators-utils[sbml,logging,containers]>=0.1.130
 ipython
 kisao
 numpy

diff --git a/tutorials/1. Introspecting models/Introspecting models.ipynb b/tutorials/1. Introspecting models/Introspecting models.ipynb
@@ -68,44 +68,44 @@
      "text": [
       "Invalid -W option ignored: invalid module name: 'biosimulators_utils.warnings'\n",
       "Defaulting to user installation because normal site-packages is not writeable\n",
-      "Requirement already satisfied: biosimulators-utils[sbml] in /usr/local/lib/python3.9/site-packages (0.1.128)\n",
-      "Requirement already satisfied: python-dateutil in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.8.2)\n",
-      "Requirement already satisfied: matplotlib in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.2.0)\n",
-      "Requirement already satisfied: termcolor in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.1.0)\n",
-      "Requirement already satisfied: biopython in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.79)\n",
-      "Requirement already satisfied: yamldown in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.1.8)\n",
+      "Requirement already satisfied: biosimulators-utils[sbml] in /usr/local/lib/python3.9/site-packages (0.1.130)\n",
+      "Requirement already satisfied: appdirs in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.4.4)\n",
+      "Requirement already satisfied: cement in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.0.4)\n",
       "Requirement already satisfied: kisao>=2.29 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.29)\n",
+      "Requirement already satisfied: pyomexmeta>=1.2.13 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.2.13)\n",
       "Requirement already satisfied: openpyxl in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.0.9)\n",
-      "Requirement already satisfied: rdflib in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (6.0.1)\n",
+      "Requirement already satisfied: validators in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.18.2)\n",
+      "Requirement already satisfied: requests-cache in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.8.2.dev1)\n",
+      "Requirement already satisfied: yamldown in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.1.8)\n",
+      "Requirement already satisfied: matplotlib in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.2.0)\n",
       "Requirement already satisfied: setuptools in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (57.5.0)\n",
-      "Requirement already satisfied: mpmath in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.2.1)\n",
-      "Requirement already satisfied: pyomexmeta>=1.2.13 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.2.13)\n",
-      "Requirement already satisfied: lxml in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (4.6.3)\n",
-      "Requirement already satisfied: evalidate in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.7.8)\n",
-      "Requirement already satisfied: python-libcombine>=0.2.11 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.2.13)\n",
+      "Requirement already satisfied: biopython in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.79)\n",
       "Requirement already satisfied: pyyaml in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (6.0b1)\n",
-      "Requirement already satisfied: h5py in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.4.0)\n",
+      "Requirement already satisfied: rdflib in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (6.0.1)\n",
       "Requirement already satisfied: pandas in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.3.3)\n",
+      "Requirement already satisfied: evalidate in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.7.8)\n",
+      "Requirement already satisfied: pronto>=2.4 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.4.3)\n",
+      "Requirement already satisfied: python-libcombine>=0.2.11 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.2.13)\n",
       "Requirement already satisfied: natsort in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (7.1.1)\n",
-      "Requirement already satisfied: cement in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.0.4)\n",
-      "Requirement already satisfied: appdirs in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.4.4)\n",
-      "Requirement already satisfied: validators in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.18.2)\n",
+      "Requirement already satisfied: numpy in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.19.3)\n",
       "Requirement already satisfied: simplejson in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.17.5)\n",
+      "Requirement already satisfied: python-dateutil in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.8.2)\n",
       "Requirement already satisfied: requests in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.26.0)\n",
-      "Requirement already satisfied: requests-cache in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (0.8.2.dev1)\n",
-      "Requirement already satisfied: numpy in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.19.3)\n",
-      "Requirement already satisfied: pronto>=2.4 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.4.3)\n",
-      "Requirement already satisfied: networkx>=2.6 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.6.3)\n",
       "Requirement already satisfied: python-libsedml>=2.0.16 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.0.26)\n",
+      "Requirement already satisfied: mpmath in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.2.1)\n",
+      "Requirement already satisfied: h5py in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (3.4.0)\n",
+      "Requirement already satisfied: networkx>=2.6 in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (2.6.3)\n",
+      "Requirement already satisfied: termcolor in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (1.1.0)\n",
+      "Requirement already satisfied: lxml in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (4.6.3)\n",
       "Requirement already satisfied: python-libsbml in /usr/local/lib/python3.9/site-packages (from biosimulators-utils[sbml]) (5.19.0)\n",
-      "Requirement already satisfied: chardet<5.0,>=3.0 in /usr/local/lib/python3.9/site-packages (from pronto>=2.4->biosimulators-utils[sbml]) (4.0.0)\n",
       "Requirement already satisfied: fastobo~=0.10.0 in /usr/local/lib/python3.9/site-packages (from pronto>=2.4->biosimulators-utils[sbml]) (0.10.2.post1)\n",
+      "Requirement already satisfied: chardet<5.0,>=3.0 in /usr/local/lib/python3.9/site-packages (from pronto>=2.4->biosimulators-utils[sbml]) (4.0.0)\n",
       "Requirement already satisfied: pydot>=1.4.1 in /usr/local/lib/python3.9/site-packages (from pyomexmeta>=1.2.13->biosimulators-utils[sbml]) (1.4.2)\n",
       "Requirement already satisfied: graphviz>=0.15 in /usr/local/lib/python3.9/site-packages (from pyomexmeta>=1.2.13->biosimulators-utils[sbml]) (0.17)\n",
       "Requirement already satisfied: pyparsing>=2.1.4 in /usr/local/lib/python3.9/site-packages (from pydot>=1.4.1->pyomexmeta>=1.2.13->biosimulators-utils[sbml]) (3.0.0rc2)\n",
       "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.9/site-packages (from python-dateutil->biosimulators-utils[sbml]) (1.16.0)\n",
-      "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.9/site-packages (from matplotlib->biosimulators-utils[sbml]) (0.10.0)\n",
       "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.9/site-packages (from matplotlib->biosimulators-utils[sbml]) (1.3.2)\n",
+      "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.9/site-packages (from matplotlib->biosimulators-utils[sbml]) (0.10.0)\n",
       "Requirement already satisfied: et-xmlfile in /usr/local/lib/python3.9/site-packages (from openpyxl->biosimulators-utils[sbml]) (1.1.0)\n",
       "Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.9/site-packages (from pandas->biosimulators-utils[sbml]) (2021.3)\n",
       "Requirement already satisfied: isodate in /usr/local/lib/python3.9/site-packages (from rdflib->biosimulators-utils[sbml]) (0.6.0)\n",
@@ -114,8 +114,8 @@
       "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.9/site-packages (from requests->biosimulators-utils[sbml]) (2021.5.30)\n",
       "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.9/site-packages (from requests->biosimulators-utils[sbml]) (3.2)\n",
       "Requirement already satisfied: url-normalize<2.0,>=1.4 in /usr/local/lib/python3.9/site-packages (from requests-cache->biosimulators-utils[sbml]) (1.4.3)\n",
-      "Requirement already satisfied: cattrs<2.0,>=1.8 in /usr/local/lib/python3.9/site-packages (from requests-cache->biosimulators-utils[sbml]) (1.8.0)\n",
       "Requirement already satisfied: attrs<22.0,>=21.2 in /usr/local/lib/python3.9/site-packages (from requests-cache->biosimulators-utils[sbml]) (21.2.0)\n",
+      "Requirement already satisfied: cattrs<2.0,>=1.8 in /usr/local/lib/python3.9/site-packages (from requests-cache->biosimulators-utils[sbml]) (1.8.0)\n",
       "Requirement already satisfied: decorator>=3.4.0 in /usr/local/lib/python3.9/site-packages (from validators->biosimulators-utils[sbml]) (5.1.0)\n"
      ]
     }
@@ -705,7 +705,9 @@
    "id": "5a97013e-d15b-427b-a011-8fb29a57eb87",
    "metadata": {},
    "source": [
-    "All model formats contain information about parameters and variables. However, most model formats such as SBML do not contain any information about simulations and plots."
+    "<div class=\"alert alert-block alert-info\">\n",
+    "    All model formats contain information about parameters and variables. However, most model formats, such as SBML, do not contain any information about simulations and plots.\n",
+    "</div>"
    ]
   },
   {