update pyproject.toml #6

dev/CB_test_modules.ipynb

@@ -1184,18 +1184,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/brune/miniconda3/envs/sprg/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2:\n",
-      "* 'underscore_attrs_are_private' has been removed\n",
-      "  warnings.warn(message, UserWarning)\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -1210,7 +1201,7 @@
       "# filter by PID\n",
       "# ------------------\n",
       "\t4867 set as 1 (= homologs), 310 set as 0 \n",
-      "\ttotal time: 0.0006549358367919922s\n",
+      "\ttotal time: 0.0005040168762207031s\n",
       "\n",
       "# --------------------\n",
       "# generate draft model\n",
@@ -1233,8 +1224,8 @@
       "\tremoved 51 non-essential genes\n",
       "\tkept 1 essential genes\n",
       "\t...................................................................\n",
-      "\ttotal time: 13.151279926300049s\n",
-      "total runtime: 15.58186388015747\n"
+      "\ttotal time: 14.834256172180176s\n",
+      "total runtime: 17.36783790588379\n"
      ]
     }
    ],
@@ -2666,6 +2657,101 @@
     "### Test Area 51"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "        <table>\n",
+       "            <tr>\n",
+       "                <td><strong>Name</strong></td>\n",
+       "                <td>test_kp</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Memory address</strong></td>\n",
+       "                <td>2d60c2ad0</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Number of metabolites</strong></td>\n",
+       "                <td>1885</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Number of reactions</strong></td>\n",
+       "                <td>2940</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Number of genes</strong></td>\n",
+       "                <td>2002</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Number of groups</strong></td>\n",
+       "                <td>0</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Objective expression</strong></td>\n",
+       "                <td>1.0*Growth - 1.0*Growth_reverse_699ae</td>\n",
+       "            </tr><tr>\n",
+       "                <td><strong>Compartments</strong></td>\n",
+       "                <td>cytosol, periplasm, extracellular space</td>\n",
+       "            </tr>\n",
+       "          </table>"
+      ],
+      "text/plain": [
+       "<Model test_kp at 0x2d60c2ad0>"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from refinegems.utility.io import load_model\n",
+    "\n",
+    "mod = load_model('/Users/brune/Documents/11_Test_Data/test_SPECIMEN/testing/test_kp_draft.xml','cobra')\n",
+    "\n",
+    "mod"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'Genome-scale metabolic model of K. pneumoniae HS11286'"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mod.name"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'optimal'"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "res = mod.optimize()\n",
+    "res.status"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -2690,7 +2776,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -7,39 +7,49 @@ name = 'specimen'
 authors = [
   { name="Carolin Brune"},
 ]
-description = ""
+description = "SPECIMEN: A package for strain-specific metabolic modelling."
 readme = "README.md"
 version = "1.0.0"
 requires-python = ">=3.10"
-#keywords = []
-#license = {}
+license = {text = "GPL-3.0"}
+keywords = ['Systems Biology', 'GEM', 'Metabolic Modelling', 'Python Package', 'Pipeline']
+
 classifiers = [
-    "Programming Language :: Python :: 3.10",
     'Operating System :: MacOS',
-    "Operating System :: Unix" # make it OS independant  - main problem currently are the paths
+    "Operating System :: Unix", # @TODO make it OS independant  - testing remains
+    # 'Operating System :: OS Independent'
+    'Programming Language :: Python',
+    # Topic :: Software Development :: Libraries :: Python Modules
+    'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)'
 ]
+
 dependencies = [
     'biopython',
+    'bofdat', # but does not work like this!!!
     'click',
     'cobra',
-    'python-libsbml',
-    # MCC@git+https://github.com/Biomathsys/MassChargeCuration
     'matplotlib',
+    'MCC@git+https://github.com/Biomathsys/MassChargeCuration', # @TODO test if it works
     'memote',
     'numpy',
     'pandas',
+    'python-libsbml',
+    'pyyaml',
     'refinegems >= 2.0',
     'requests',
     'SBOannotator',
     'seaborn',
     'tqdm',
-    'pyyaml',
     'z3-solver'
 ]
 # additional missing tools:
 #    EntrezDirect
 #    DIAMOND
-#    BOFdat
+
+# @TODO:
+[project.urls]
+homepage = 'https://github.com/draeger-lab/SPECIMEN'
+# documentation = 
 
 [project.scripts]
 specimen = "specimen.cmd_access:cli"