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Merged
merged 10 commits into from
Feb 3, 2025
Merged

Update footer img #53

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f02e2d6
🙈 Docs: update .gitignore file
sayalaruano Jan 31, 2025
a129950
Merge branch 'main' of https://github.com/Multiomics-Analytics-Group/…
sayalaruano Jan 31, 2025
db6df32
📝 Docs(README.md): Update image links and installation instructions o…
sayalaruano Jan 31, 2025
68ee76e
🔀 Merge changes from github repo
sayalaruano Jan 31, 2025
1f5330f
🐛 Fix: Add vuegen logo in the footer of reports from url and add smal…
sayalaruano Jan 31, 2025
97182e3
👷 CI: Add html report code and results to build report example web page
sayalaruano Jan 31, 2025
fa32cd3
💚 CI: Comment code to generate revelajs report on the demo notebook t…
sayalaruano Feb 3, 2025
9885993
🐛 Fix(vuegen_case_study_earth_microbiome.ipynb): Read EMP logo from u…
sayalaruano Feb 3, 2025
9d2f9cc
Merge branch 'main' into update-footer-img
enryH Feb 3, 2025
7034c49
:bug: html report (typo)
enryH Feb 3, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -128,5 +128,5 @@ docs/images/Graphical_abstract/
docs/images/Nfcore_module_figure
docs/presentations/
docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/
docs/vuegen_case_study_earth_microbiome test.ipynb
docs/vuegen_case_study_earth_microbiome_test.ipynb
test.py
Binary file modified docs/images/vuegen_classdiagram_noattmeth.png
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4,741 changes: 2,367 additions & 2,374 deletions docs/images/vuegen_logo.svg
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115 changes: 86 additions & 29 deletions docs/vuegen_case_study_earth_microbiome.ipynb
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Expand Up @@ -65,8 +65,18 @@
"metadata": {},
"outputs": [],
"source": [
"# Install required libraries\n",
"%pip install vuegen cartopy seaborn biom-format"
"# Vuegen library \n",
"%pip install vuegen"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Libraries for the notebook\n",
"%pip install cartopy seaborn biom-format"
]
},
{
Expand All @@ -78,7 +88,7 @@
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -113,7 +123,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -132,7 +142,7 @@
},
{
"cell_type": "code",
"execution_count": 29,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -160,7 +170,7 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -234,7 +244,7 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -257,7 +267,7 @@
},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -489,7 +499,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -504,7 +514,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -712,7 +722,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -729,7 +739,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -867,7 +877,7 @@
},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -896,7 +906,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -1146,7 +1156,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1168,7 +1178,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1190,7 +1200,7 @@
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1210,7 +1220,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": 27,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1230,7 +1240,7 @@
},
{
"cell_type": "code",
"execution_count": 29,
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1247,7 +1257,7 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -1343,7 +1353,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1355,7 +1365,30 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### 4.2. HTML report"
"### 4.2. Revealjs report"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [],
"source": [
"# report_type = \"revealjs\"\n",
"# report_name = \"Earth_microbiome_vuegen_demo_notebook_dir\"\n",
"\n",
"# Initialize logger\n",
"# logger = get_logger(f\"{report_type}_report_{report_name}\")\n",
"\n",
"# Generate the report\n",
"# report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = logger)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 4.3. HTML report"
]
},
{
Expand Down Expand Up @@ -1391,11 +1424,11 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 36,
"metadata": {},
"outputs": [],
"source": [
"empo_logo_path = os.path.join(base_output_dir, \"emp_logo.png\")\n",
"empo_logo_path = \"https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg\"\n",
"\n",
"# Load the YAML file\n",
"config_path = os.path.join(base_output_dir, \"Earth_microbiome_vuegen_demo_notebook_config.yaml\")\n",
Expand All @@ -1414,7 +1447,7 @@
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 37,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1440,7 +1473,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -1471,7 +1504,7 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 39,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -1528,7 +1561,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1540,7 +1573,31 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### 5.6. HTML report with the extended configuration file"
"### 5.6. Revealjs report with the extended configuration file"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"# Test the changes by generarating the report from the modified YAML file\n",
"# report_type = \"revealjs\"\n",
"# report_name = \"Earth_microbiome_vuegen_demo_notebook_config_extended\"\n",
"\n",
"# Initialize logger\n",
"# logger = get_logger(f\"{report_type}_report_{report_name}\")\n",
"\n",
"# Generate the report\n",
"# report_generator.get_report(config_path = config_path, report_type = report_type, logger = logger)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 5.7. HTML report with the extended configuration file"
]
},
{
Expand Down
4 changes: 2 additions & 2 deletions src/vuegen/quarto_reportview.py
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Expand Up @@ -172,7 +172,7 @@ def _create_yaml_header(self) -> str:
<footer class="footer">
This report was generated with
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
<img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
</a>
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
</footer>""",
Expand Down Expand Up @@ -218,7 +218,7 @@ def _create_yaml_header(self) -> str:
<footer class="footer">
This report was generated with
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
<img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
</a>
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
</footer>""",
Expand Down
2 changes: 1 addition & 1 deletion src/vuegen/utils.py
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Expand Up @@ -738,7 +738,7 @@ def generate_footer() -> str:
<footer class="footer">
This report was generated with
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
<img src="../../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
</a>
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">
Multiomics Network Analytics Group (MoNA)
Expand Down