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💥 Write config file based on directory to output directory of report
- read-only situation of result directories: One cannot always write to directory which contains the results if -dir option is used - ✨ Return paths for easier reporting - adapt example notebooks accordingly
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6 files changed

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lines changed

‎docs/vuegen_basic_case_study.ipynb‎

Lines changed: 15 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -164,22 +164,18 @@
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"source": [
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"# Generate the report\n",
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"report_type = \"streamlit\"\n",
167-
"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
167+
"report_dir, config_path = report_generator.get_report(\n",
168+
" dir_path=base_output_dir, report_type=report_type, logger=None\n",
169+
")\n",
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"print(f\"\\nReport generated in {report_dir}\")\n",
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"print(f\"\\nConfig file generated in {config_path}\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Streamlit report not executed, set run_streamlit to True to run the report\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"run_streamlit = False\n",
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"# run_streamlit = True # uncomment line to run the streamlit report\n",
@@ -212,7 +208,8 @@
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"source": [
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"# Generate the report\n",
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"report_type = \"html\"\n",
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"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
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"report_dir, config_path = report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)\n",
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"print(f\"Report generated at: {report_dir}\")"
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]
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},
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{
@@ -232,14 +229,14 @@
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg\"\n",
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"\n",
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"# Load the YAML file\n",
242-
"config_path = os.path.join(base_output_dir, \"Basic_example_vuegen_demo_notebook_config.yaml\")\n",
239+
"print(f\"Loading the YAML config file from: {config_path}\") # generated based on directory path above\n",
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"config = load_yaml_config(config_path)\n",
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"\n",
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"# Update the logo and graphical abstract with the URL\n",
@@ -255,7 +252,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 21,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -281,7 +278,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 22,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -324,7 +321,7 @@
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"source": [
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"# Test the changes by generarating the report from the modified YAML file\n",
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"report_type = \"streamlit\"\n",
327-
"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
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"_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
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]
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},
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{
@@ -364,7 +361,7 @@
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"source": [
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"# Test the changes by generarating the report from the modified YAML file\n",
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"report_type = \"html\"\n",
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"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
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"_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
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]
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}
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],

‎docs/vuegen_case_study_earth_microbiome.ipynb‎

Lines changed: 27 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 27,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -179,7 +179,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 29,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -207,7 +207,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 30,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -281,7 +281,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 31,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -304,7 +304,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 32,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -536,7 +536,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -759,7 +759,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -776,7 +776,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -914,7 +914,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 33,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 34,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1193,7 +1193,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 25,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1215,7 +1215,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 26,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1237,7 +1237,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 27,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1257,7 +1257,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 28,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1277,7 +1277,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 29,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1294,7 +1294,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 30,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1382,7 +1382,7 @@
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"source": [
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"# Generate the report\n",
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"report_type = \"streamlit\"\n",
1385-
"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
1385+
"_ = report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
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]
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},
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{
@@ -1422,7 +1422,9 @@
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"source": [
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"# Generate the report\n",
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"report_type = \"html\"\n",
1425-
"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
1425+
"report_dir, config_path = report_generator.get_report(\n",
1426+
" dir_path=base_output_dir, report_type=report_type, logger=None\n",
1427+
")"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"empo_logo_path = \"https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg\"\n",
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"\n",
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"# Load the YAML file\n",
1452-
"config_path = os.path.join(base_output_dir, \"Earth_microbiome_vuegen_demo_notebook_config.yaml\")\n",
14531454
"config = load_yaml_config(config_path)\n",
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"\n",
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"# Update the logo and graphical abstract with the URL\n",
@@ -1465,7 +1466,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 21,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 22,
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"execution_count": null,
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"metadata": {},
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 23,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -1570,7 +1571,7 @@
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"source": [
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"# Test the changes by generarating the report from the modified YAML file\n",
15721573
"report_type = \"streamlit\"\n",
1573-
"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
1574+
"_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
15741575
]
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},
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{
@@ -1610,7 +1611,7 @@
16101611
"source": [
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"# Test the changes by generarating the report from the modified YAML file\n",
16121613
"report_type = \"html\"\n",
1613-
"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
1614+
"_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
16141615
]
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}
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],

‎gui/app.py‎

Lines changed: 9 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -53,6 +53,8 @@
5353
app_path.parent / "example_data/Basic_example_vuegen_demo_notebook"
5454
).resolve()
5555
quarto_bin_path = os.path.join(sys._MEIPASS, "quarto_cli", "bin")
56+
# /.venv/lib/python3.12/site-packages/quarto_cli/bin
57+
# source activate .venv/bin/activate
5658
quarto_share_path = os.path.join(sys._MEIPASS, "quarto_cli", "share")
5759
_PATH = os.pathsep.join([quarto_bin_path, quarto_share_path, _PATH])
5860
os.environ["PATH"] = _PATH
@@ -146,10 +148,14 @@ def inner():
146148
kwargs["logger"].info("logfile: %s", log_file)
147149
kwargs["logger"].debug("sys.path: %s", sys.path)
148150
kwargs["logger"].debug("PATH (in app): %s ", os.environ["PATH"])
149-
report_generator.get_report(**kwargs)
151+
report_dir, gen_config_path = report_generator.get_report(**kwargs)
152+
kwargs["logger"].info("Report generated at %s", report_dir)
150153
messagebox.showinfo(
151154
"Success",
152-
"Report generation completed successfully." f"\nLogs at {log_file}",
155+
"Report generation completed successfully."
156+
f"\n\nLogs at:\n{log_file}"
157+
f"\n\nReport in folder:\n{report_dir}"
158+
f"\n\nConfiguration file at:\n{gen_config_path}",
153159
)
154160
print_completion_message(report_type.get())
155161
except Exception as e:
@@ -245,7 +251,7 @@ def select_directory():
245251
ctk_label_report.grid(row=row_count, column=0, columnspan=2, padx=20, pady=20)
246252
row_count += 1
247253
##########################################################################################
248-
report_type = tk.StringVar(value=report_types[0])
254+
report_type = tk.StringVar(value=report_types[1])
249255
report_dropdown = customtkinter.CTkOptionMenu(
250256
app,
251257
values=report_types,

‎src/vuegen/__main__.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ def main():
3939
logger, logfile = get_logger(f"{logger_suffix}")
4040
logger.info("logfile: %s", logfile)
4141
# Generate the report
42-
report_generator.get_report(
42+
_, _ = report_generator.get_report(
4343
report_type=report_type,
4444
logger=logger,
4545
config_path=config_path,
@@ -48,6 +48,7 @@ def main():
4848
)
4949

5050
# Print completion message
51+
# ! Could use now report_dir and config_path as information
5152
print_completion_message(report_type)
5253

5354

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