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Merged
JoshuaHarris391 merged 3 commits into from
Aug 12, 2025
Merged

Feature publish pypi on release #8

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f33f855
Update requirements.txt to remove dotenv
JoshuaHarris391 Jul 11, 2025
b181eb4
Update requirements.txt to specify exact package versions for consist…
JoshuaHarris391 Jul 11, 2025
0107a55
first attempt at packaging, v1.1.0 successfully published to pypi
JoshuaHarris391 Jul 11, 2025
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2 changes: 1 addition & 1 deletion build.sh
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

#!/bin/bash
python -m venv .venv
source venv/bin/activate
source .venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
pip install -e .
115 changes: 107 additions & 8 deletions example_notebook.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,20 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 7,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"<Logger gen3_metadata (INFO)>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from gen3_metadata.logger import setup_logger\n",
"from gen3_metadata.gen3_metadata_parser import Gen3MetadataParser\n",
Expand All @@ -22,7 +33,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -33,23 +44,111 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"File not found: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"An unexpected error occurred during authentication: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"Unexpected exception formatting exception. Falling back to standard exception\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 3550, in run_code\n",
" File \"/var/folders/h1/smw4rryj4zs361v4bw9qqc0c0000gn/T/ipykernel_58301/122813687.py\", line 2, in <module>\n",
" gen3metadata.authenticate()\n",
" File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 110, in authenticate\n",
" key = self._load_api_key()\n",
" File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 60, in _load_api_key\n",
" with open(self.key_file_path, \"r\") as f:\n",
"FileNotFoundError: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 45, in get_style_by_name\n",
"ModuleNotFoundError: No module named 'pygments.styles.default'\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 2144, in showtraceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1435, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1326, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1173, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1063, in format_exception_as_a_whole\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1114, in get_records\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 47, in get_style_by_name\n",
"pygments.util.ClassNotFound: Could not find style module 'pygments.styles.default', though it should be builtin.\n"
]
}
],
"source": [
"# Authenticate\n",
"gen3metadata.authenticate()"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"File not found: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"An error occurred: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"Unexpected exception formatting exception. Falling back to standard exception\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 3550, in run_code\n",
" File \"/var/folders/h1/smw4rryj4zs361v4bw9qqc0c0000gn/T/ipykernel_58301/3932466949.py\", line 4, in <module>\n",
" gen3metadata.fetch_data_pd(program_name, project_code, node_label= \"medical_history\")\n",
" File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 256, in fetch_data_pd\n",
" data = self.fetch_data(program_name, project_code, node_label, api_version=api_version, return_data=True)\n",
" File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 185, in fetch_data\n",
" creds = self._load_api_key()\n",
" File \"/Users/harrijh/projects/gen3-metadata/src/gen3metadata/gen3_metadata_parser.py\", line 60, in _load_api_key\n",
" with open(self.key_file_path, \"r\") as f:\n",
"FileNotFoundError: [Errno 2] No such file or directory: 'path/to/credentials.json'\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 45, in get_style_by_name\n",
"ModuleNotFoundError: No module named 'pygments.styles.default'\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 2144, in showtraceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1435, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1326, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1173, in structured_traceback\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1063, in format_exception_as_a_whole\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1114, in get_records\n",
" File \"/Users/harrijh/projects/gen3-metadata/.venv/lib/python3.9/site-packages/pygments/styles/__init__.py\", line 47, in get_style_by_name\n",
"pygments.util.ClassNotFound: Could not find style module 'pygments.styles.default', though it should be builtin.\n"
]
}
],
"source": [
"# fetching data and returning as dataframe\n",
"program_name= \"program1\"\n",
"project_code= \"project1\"\n",
"project_code= \"AusDiab_Simulated\"\n",
"gen3metadata.fetch_data_pd(program_name, project_code, node_label= \"medical_history\")"
]
},
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