Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Doc: fix deprecated petablint invocation #343

Merged
merged 2 commits into from
Dec 16, 2024
Merged

Doc: fix deprecated petablint invocation #343

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
744d01e
Doc: fix deprecated petablint invocation
dweindl Dec 16, 2024
578c527
Merge branch 'develop' into fix_petab592
dweindl Dec 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
79 changes: 10 additions & 69 deletions doc/example/example_petablint.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,75 +16,26 @@
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"usage: petablint [-h] [-v] [-s SBML_FILE_NAME] [-m MEASUREMENT_FILE_NAME]\r\n",
" [-c CONDITION_FILE_NAME] [-p PARAMETER_FILE_NAME]\r\n",
" [-y YAML_FILE_NAME | -n MODEL_NAME] [-d DIRECTORY]\r\n",
"\r\n",
"Check if a set of files adheres to the PEtab format.\r\n",
"\r\n",
"optional arguments:\r\n",
" -h, --help show this help message and exit\r\n",
" -v, --verbose More verbose output\r\n",
" -s SBML_FILE_NAME, --sbml SBML_FILE_NAME\r\n",
" SBML model filename\r\n",
" -m MEASUREMENT_FILE_NAME, --measurements MEASUREMENT_FILE_NAME\r\n",
" Measurement table\r\n",
" -c CONDITION_FILE_NAME, --conditions CONDITION_FILE_NAME\r\n",
" Conditions table\r\n",
" -p PARAMETER_FILE_NAME, --parameters PARAMETER_FILE_NAME\r\n",
" Parameter table\r\n",
" -y YAML_FILE_NAME, --yaml YAML_FILE_NAME\r\n",
" PEtab YAML problem filename\r\n",
" -n MODEL_NAME, --model-name MODEL_NAME\r\n",
" Model name where all files are in the working\r\n",
" directory and follow PEtab naming convention.\r\n",
" Specifying -[smcp] will override defaults\r\n",
" -d DIRECTORY, --directory DIRECTORY\r\n"
]
}
],
"source": [
"!petablint -h"
]
],
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's look at an example: In the example_Fujita folder, we have a PEtab configuration file `Fujita.yaml` telling which files belong to the Fujita model:"
]
"source": "Let's look at an example: In the `example_Fujita/` directory, we have a PEtab problem configuration file `Fujita.yaml` telling which files belong to the \"Fujita\" problem:"
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"parameter_file: Fujita_parameters.tsv\r\n",
"petab_version: 0.0.0a17\r\n",
"problems:\r\n",
"- condition_files:\r\n",
" - Fujita_experimentalCondition.tsv\r\n",
" measurement_files:\r\n",
" - Fujita_measurementData.tsv\r\n",
" sbml_files:\r\n",
" - Fujita_model.xml\r\n"
]
}
],
"source": [
"!cat example_Fujita/Fujita.yaml"
]
],
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -95,20 +46,10 @@
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0m"
]
}
],
"source": [
"!petablint -y example_Fujita/Fujita.yaml"
]
"source": "!petablint example_Fujita/Fujita.yaml",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand Down
Loading