diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
index 658090541..307830958 100644
--- a/notebooks/copasi_process_composer.ipynb
+++ b/notebooks/copasi_process_composer.ipynb
@@ -17,8 +17,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-03-04T17:50:00.677085Z",
- "start_time": "2024-03-04T17:50:00.673697Z"
+ "end_time": "2024-03-04T18:12:46.780098Z",
+ "start_time": "2024-03-04T18:12:46.776381Z"
}
},
"outputs": [],
@@ -51,8 +51,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-03-04T17:50:02.887453Z",
- "start_time": "2024-03-04T17:50:01.104405Z"
+ "end_time": "2024-03-04T18:13:02.776479Z",
+ "start_time": "2024-03-04T18:12:47.630719Z"
}
},
"id": "65385e04f4f5dd1a",
@@ -70,14 +70,10 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"id": "cc709690e20090cf",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:02.888217Z",
- "start_time": "2024-03-04T17:50:02.886116Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -106,25 +102,12 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"id": "edf123175ec3408c",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:04.622174Z",
- "start_time": "2024-03-04T17:50:04.614887Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "data": {
- "text/plain": "True"
- },
- "execution_count": 4,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"model_filepath = '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'\n",
"\n",
@@ -133,14 +116,10 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"id": "40ab6f70ac3f4996",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:05.248267Z",
- "start_time": "2024-03-04T17:50:05.244475Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -151,31 +130,12 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"id": "d02a547b85138f96",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:05.763539Z",
- "start_time": "2024-03-04T17:50:05.760973Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'global_parameter_changes': [],\n",
- " 'reaction_changes': [],\n",
- " 'species_changes': [ { 'expression': '',\n",
- " 'initial_concentration': 9.261000000000001,\n",
- " 'initial_expression': '',\n",
- " 'initial_particle_number': None,\n",
- " 'name': 'ADP',\n",
- " 'unit': ''}]}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# 1. specify model changes (we know the model specs as we are providing the file. TODO: allow users to introspect the model before change)\n",
"process_model_changes = ModelChanges(\n",
@@ -188,36 +148,12 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"id": "1b6c269646357d7d",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:06.373209Z",
- "start_time": "2024-03-04T17:50:06.370745Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'model_changes': { 'global_parameter_changes': [],\n",
- " 'reaction_changes': [],\n",
- " 'species_changes': [ { 'expression': '',\n",
- " 'initial_concentration': 9.261000000000001,\n",
- " 'initial_expression': '',\n",
- " 'initial_particle_number': None,\n",
- " 'name': 'ADP',\n",
- " 'unit': ''}]},\n",
- " 'model_id': 'copasi_process_from_file',\n",
- " 'model_language': 'sbml',\n",
- " 'model_name': 'Simple Composite Process from File',\n",
- " 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
- " 'model_units': None}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# 2. define the model schema to be used by the composite process (one of the copasiprocess config parameters)\n",
"\n",
@@ -234,38 +170,12 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"id": "5d434956e65b1a42",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:06.867692Z",
- "start_time": "2024-03-04T17:50:06.856103Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'method': 'stochastic',\n",
- " 'model': { 'model_changes': { 'global_parameter_changes': [],\n",
- " 'reaction_changes': [],\n",
- " 'species_changes': [ { 'expression': '',\n",
- " 'initial_concentration': 9.261000000000001,\n",
- " 'initial_expression': '',\n",
- " 'initial_particle_number': None,\n",
- " 'name': 'ADP',\n",
- " 'unit': ''}]},\n",
- " 'model_id': 'copasi_process_from_file',\n",
- " 'model_language': 'sbml',\n",
- " 'model_name': 'Simple Composite Process from File',\n",
- " 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
- " 'model_units': None},\n",
- " 'process_name': 'simple_copasi_from_file'}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# 3. Define config schema to be used as 'config' parameter of Process constructor\n",
"process_config_from_file = CopasiProcessConfigSchema(\n",
@@ -280,39 +190,22 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": null,
"id": "de88e95d8f616779",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:07.430573Z",
- "start_time": "2024-03-04T17:50:07.417667Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "data": {
- "text/plain": "{'model_id': 'copasi_process_from_file',\n 'model_source': {'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n 'model_language': 'sbml',\n 'model_name': 'Simple Composite Process from File',\n 'model_changes': {'species_changes': [{'name': 'ADP',\n 'unit': '',\n 'initial_concentration': 9.261000000000001,\n 'initial_particle_number': None,\n 'initial_expression': '',\n 'expression': ''}],\n 'global_parameter_changes': [],\n 'reaction_changes': []},\n 'model_units': None}"
- },
- "execution_count": 9,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"process_config_from_file.model"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"id": "52d81ea2ea688d47",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:08.032162Z",
- "start_time": "2024-03-04T17:50:07.858962Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -338,14 +231,10 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": null,
"id": "f499f96a817d9faf",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:09.130046Z",
- "start_time": "2024-03-04T17:50:09.127179Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -361,14 +250,10 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": null,
"id": "c24594c6e8229e20",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:09.703656Z",
- "start_time": "2024-03-04T17:50:09.699035Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -379,14 +264,10 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": null,
"id": "454db50d61220bc5",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:10.125789Z",
- "start_time": "2024-03-04T17:50:10.122877Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -413,14 +294,10 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": null,
"id": "bd6781fe4a749c29",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:10.818914Z",
- "start_time": "2024-03-04T17:50:10.816816Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -431,73 +308,24 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": null,
"id": "e414174a2d6d331b",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:11.493997Z",
- "start_time": "2024-03-04T17:50:11.486528Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'global_parameter_changes': [],\n",
- " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
- " 'value': 21312.2},\n",
- " { 'parameter_name': 'EpoRJAK2',\n",
- " 'value': 21312.2}],\n",
- " 'reaction_name': 'reaction_1',\n",
- " 'reaction_scheme': None},\n",
- " { 'parameter_changes': [],\n",
- " 'reaction_name': 'reaction_11',\n",
- " 'reaction_scheme': 'A + B -> C'}],\n",
- " 'species_changes': []}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"pp(biomodel_process_changes.model_dump())"
]
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": null,
"id": "9de88bc52fb9a164",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:12.301630Z",
- "start_time": "2024-03-04T17:50:12.297923Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'model_changes': { 'global_parameter_changes': [],\n",
- " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
- " 'value': 21312.2},\n",
- " { 'parameter_name': 'EpoRJAK2',\n",
- " 'value': 21312.2}],\n",
- " 'reaction_name': 'reaction_1',\n",
- " 'reaction_scheme': None},\n",
- " { 'parameter_changes': [],\n",
- " 'reaction_name': 'reaction_11',\n",
- " 'reaction_scheme': 'A + B -> C'}],\n",
- " 'species_changes': []},\n",
- " 'model_id': 'BIOMD0000000861',\n",
- " 'model_language': 'sbml',\n",
- " 'model_name': 'composite_from_biomodel',\n",
- " 'model_source': {'value': 'BIOMD0000000861'},\n",
- " 'model_units': None}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"biomodel_id = 'BIOMD0000000861'\n",
"\n",
@@ -514,45 +342,12 @@
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": null,
"id": "25ba11c1e1e75f94",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:13.242111Z",
- "start_time": "2024-03-04T17:50:13.238863Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "{ 'method': 'directMethod',\n",
- " 'model': { 'model_changes': { 'global_parameter_changes': [],\n",
- " 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
- " 'value': 21312.2},\n",
- " { 'parameter_name': 'EpoRJAK2',\n",
- " 'value': 21312.2}],\n",
- " 'reaction_name': 'reaction_1',\n",
- " 'reaction_scheme': None},\n",
- " { 'parameter_changes': [],\n",
- " 'reaction_name': 'reaction_11',\n",
- " 'reaction_scheme': 'A '\n",
- " '+ '\n",
- " 'B '\n",
- " '-> '\n",
- " 'C'}],\n",
- " 'species_changes': []},\n",
- " 'model_id': 'BIOMD0000000861',\n",
- " 'model_language': 'sbml',\n",
- " 'model_name': 'composite_from_biomodel',\n",
- " 'model_source': {'value': 'BIOMD0000000861'},\n",
- " 'model_units': None},\n",
- " 'process_name': 'copasi_process_from_biomodel'}\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"biomodel_process_config = CopasiProcessConfigSchema(\n",
" process_name='copasi_process_from_biomodel',\n",
@@ -576,14 +371,10 @@
},
{
"cell_type": "code",
- "execution_count": 18,
+ "execution_count": null,
"id": "4c3f073b10e2dcc0",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:18.027839Z",
- "start_time": "2024-03-04T17:50:15.583320Z"
- }
+ "collapsed": false
},
"outputs": [],
"source": [
@@ -606,26 +397,12 @@
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": null,
"id": "c5e03e6714faf9f4",
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:50:41.572855Z",
- "start_time": "2024-03-04T17:50:41.248206Z"
- }
+ "collapsed": false
},
- "outputs": [
- {
- "data": {
- "image/svg+xml": "\n\n\n\n\n",
- "text/plain": ""
- },
- "execution_count": 19,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"b.visualize()"
]
@@ -642,30 +419,17 @@
},
{
"cell_type": "code",
- "outputs": [
- {
- "data": {
- "text/plain": "Builder({ 'copasi_process_from_biomodel': { '_type': 'process',\n 'address': 'local:CopasiProcess',\n 'config': { 'method': 'directMethod',\n 'model': { 'model_changes': { 'global_parameter_changes': [ ],\n 'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n 'value': 21312.2},\n { 'parameter_name': 'EpoRJAK2',\n 'value': 21312.2}],\n 'reaction_name': 'reaction_1',\n 'reaction_scheme': None},\n { 'parameter_changes': [ ],\n 'reaction_name': 'reaction_11',\n 'reaction_scheme': 'A '\n '+ '\n 'B '\n '-> '\n 'C'}],\n 'species_changes': [ ]},\n 'model_id': 'BIOMD0000000861',\n 'model_language': 'sbml',\n 'model_name': 'composite_from_biomodel',\n 'model_source': { 'value': 'BIOMD0000000861'},\n 'model_units': None}},\n 'inputs': { 'floating_species': [ 'floating_species_store'],\n 'model_parameters': [ 'model_parameters_store'],\n 'reactions': [ 'reactions_store'],\n 'time': ['time_store']},\n 'instance': ,\n 'interval': 1.0,\n 'outputs': { 'floating_species': [ 'floating_species_store'],\n 'time': ['time_store']}},\n 'simple_copasi_from_file': { '_type': 'process',\n 'address': 'local:CopasiProcess',\n 'config': { 'method': 'stochastic',\n 'model': { 'model_changes': { 'global_parameter_changes': [ ],\n 'reaction_changes': [ ],\n 'species_changes': [ { 'expression': '',\n 'initial_concentration': 9.261000000000001,\n 'initial_expression': '',\n 'initial_particle_number': None,\n 'unit': ''}]},\n 'model_id': 'copasi_process_from_file',\n 'model_language': 'sbml',\n 'model_name': 'Simple '\n 'Composite '\n 'Process '\n 'from File',\n 'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n 'model_units': None}},\n 'inputs': { 'floating_species': [ 'floating_species_store'],\n 'model_parameters': [ 'model_parameters_store'],\n 'reactions': ['reactions_store'],\n 'time': ['time_store']},\n 'instance': ,\n 'interval': 1.0,\n 'outputs': { 'floating_species': [ 'floating_species_store'],\n 'time': ['time_store']}}})"
- },
- "execution_count": 27,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"b.connect_all(append_to_store_name='_store')\n",
"\n",
"b"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2024-03-04T17:53:24.749677Z",
- "start_time": "2024-03-04T17:53:24.744838Z"
- }
+ "collapsed": false
},
"id": "d9bef3f51b50fbd5",
- "execution_count": 27
+ "execution_count": null
},
{
"cell_type": "code",
diff --git a/poetry.lock b/poetry.lock
index 6e751b9ac..692296200 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -256,12 +256,12 @@ process-bigraph = "*"
[[package]]
name = "bigraph-schema"
-version = "0.0.29"
+version = "0.0.30"
description = "A serializable type schema for compositional systems biology"
optional = false
python-versions = ">=3.6"
files = [
- {file = "bigraph-schema-0.0.29.tar.gz", hash = "sha256:460bb5e2dd21c0044779024cf03a2a1b68e44f25da775f6bfc0c62ff79037667"},
+ {file = "bigraph-schema-0.0.30.tar.gz", hash = "sha256:dd7a2c047ff144f9e65236ad4cd93f51737cbefe8d1b531cf78d500e91371e38"},
]
[package.dependencies]
@@ -272,12 +272,12 @@ pytest = "*"
[[package]]
name = "bigraph-viz"
-version = "0.0.31"
+version = "0.0.33"
description = "A graphviz-based plotting tool for compositional bigraph schema"
optional = false
python-versions = ">=3.6"
files = [
- {file = "bigraph-viz-0.0.31.tar.gz", hash = "sha256:ec3c5c1a37c651fe4e0a07f01a18ba0d35c780b53557f588e9bd9080bdc50ba7"},
+ {file = "bigraph-viz-0.0.33.tar.gz", hash = "sha256:abec065149184247967c07dad0c9114a8ac379b331efebf829eecf057fe6dd9c"},
]
[package.dependencies]
@@ -1156,13 +1156,13 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
[[package]]
name = "ipython"
-version = "8.22.1"
+version = "8.22.2"
description = "IPython: Productive Interactive Computing"
optional = false
python-versions = ">=3.10"
files = [
- {file = "ipython-8.22.1-py3-none-any.whl", hash = "sha256:869335e8cded62ffb6fac8928e5287a05433d6462e3ebaac25f4216474dd6bc4"},
- {file = "ipython-8.22.1.tar.gz", hash = "sha256:39c6f9efc079fb19bfb0f17eee903978fe9a290b1b82d68196c641cecb76ea22"},
+ {file = "ipython-8.22.2-py3-none-any.whl", hash = "sha256:3c86f284c8f3d8f2b6c662f885c4889a91df7cd52056fd02b7d8d6195d7f56e9"},
+ {file = "ipython-8.22.2.tar.gz", hash = "sha256:2dcaad9049f9056f1fef63514f176c7d41f930daa78d05b82a176202818f2c14"},
]
[package.dependencies]
@@ -1275,13 +1275,13 @@ i18n = ["Babel (>=2.7)"]
[[package]]
name = "json5"
-version = "0.9.17"
+version = "0.9.20"
description = "A Python implementation of the JSON5 data format."
optional = false
python-versions = ">=3.8"
files = [
- {file = "json5-0.9.17-py2.py3-none-any.whl", hash = "sha256:f8ec1ecf985951d70f780f6f877c4baca6a47b6e61e02c4cd190138d10a7805a"},
- {file = "json5-0.9.17.tar.gz", hash = "sha256:717d99d657fa71b7094877b1d921b1cce40ab444389f6d770302563bb7dfd9ae"},
+ {file = "json5-0.9.20-py3-none-any.whl", hash = "sha256:f623485b37fad95783233bad9352d21526709cbd9a2ec41ddc3e950fca85b701"},
+ {file = "json5-0.9.20.tar.gz", hash = "sha256:20a255981244081d5aaa4adc90d31cdbf05bed1863993cbf300b8e2cd2b6de88"},
]
[package.extras]
@@ -1424,13 +1424,13 @@ jupyter-server = ">=1.1.2"
[[package]]
name = "jupyter-server"
-version = "2.12.5"
+version = "2.13.0"
description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
optional = false
python-versions = ">=3.8"
files = [
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[[package]]
name = "keyring"
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description = "Store and access your passwords safely."
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python-versions = ">=3.8"
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