diff --git a/.gitignore b/.gitignore
index 158faf3..fc36cb5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -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
\ No newline at end of file
diff --git a/docs/images/vuegen_classdiagram_noattmeth.png b/docs/images/vuegen_classdiagram_noattmeth.png
index b7c578d..ae87243 100644
Binary files a/docs/images/vuegen_classdiagram_noattmeth.png and b/docs/images/vuegen_classdiagram_noattmeth.png differ
diff --git a/docs/images/vuegen_logo.svg b/docs/images/vuegen_logo.svg
index fff2065..dbb3316 100644
--- a/docs/images/vuegen_logo.svg
+++ b/docs/images/vuegen_logo.svg
@@ -29,14 +29,14 @@
inkscape:pagecheckerboard="0"
inkscape:deskcolor="#d1d1d1"
inkscape:zoom="1.2685346"
- inkscape:cx="152.14406"
- inkscape:cy="195.89533"
+ inkscape:cx="217.17973"
+ inkscape:cy="131.25381"
inkscape:window-width="1200"
inkscape:window-height="932"
inkscape:window-x="1200"
inkscape:window-y="25"
inkscape:window-maximized="0"
- inkscape:current-layer="Layer_1"
+ inkscape:current-layer="g7"
showgrid="true"
inkscape:document-units="mm">
+
+ id="g7">
VueGen
-VueGen
+ d="m 202.91198,313.90002 c 0,-0.5 0,-1 0,-1.4 0.3,-0.2 0.2,-0.7 0.5,-1 0,-0.3 0,-0.6 0,-1 0.2,-0.1 0.3,-0.3 0.5,-0.5 0.2,-0.2 0.3,-0.3 0.5,-0.5 0.7,0.1 1.4,-0.2 1.9,0.5 0.2,0.2 0.3,0.3 0.5,0.5 1,0 1.9,0 2.9,0 0.2,-0.2 0.3,-0.3 0.5,-0.5 0.2,-0.2 0.3,-0.3 0.5,-0.5 0.3,0 0.6,0 1,0 0.6,-0.3 1.3,-0.3 1.9,0 0.2,0 0.3,0 0.5,0 0.1,0.2 0.3,0.3 0.5,0.5 0.2,0.2 0.3,0.3 0.5,0.5 0,0.2 0,0.3 0,0.5 0.3,0.6 0.3,1.3 0,1.9 0,0.2 0,0.3 0,0.5 -0.2,0.1 -0.3,0.3 -0.5,0.5 -0.4,0.8 -0.4,1.6 0,2.4 0.9,1.9 0.3,3.8 0.5,5.7 -0.4,0.4 -0.6,1 -1,1.4 0,0.6 0,1.3 0,1.9 0.3,0.5 0.3,1 0,1.4 -0.2,0.2 -0.3,0.3 -0.5,0.5 -0.2,0.2 -0.3,0.3 -0.5,0.5 0,0.2 0,0.3 0,0.5 -0.2,0.1 -0.3,0.3 -0.5,0.5 -0.2,0.2 -0.3,0.3 -0.5,0.5 -0.2,0 -0.3,0 -0.5,0 -0.2,0.2 -0.3,0.3 -0.5,0.5 0,0.8 -0.1,1.6 -1,1.9 -0.6,0.3 -1.2,0.6 -1.8,0.2 -1,-0.6 -1.8,-1.8 -3,-0.5 -0.8,0.9 -2.2,0.7 -2.8,2 -0.5,1.1 -1.3,0.9 -2,0.2 -0.1,-0.1 -0.2,-0.2 -0.1,-0.3 0,-0.1 0.1,-0.2 0.1,-0.2 0,-0.2 0,-0.3 0,-0.5 0.2,-0.1 0.3,-0.3 0.5,-0.5 0,-0.2 0,-0.3 0,-0.5 0.5,-0.5 0,-1.4 0.5,-1.9 0.2,-0.2 0.3,-0.3 0.5,-0.5 0.6,-0.5 1.4,0.1 1.9,-0.5 0.2,0 0.3,0 0.5,0 0.2,-0.2 0.3,-0.3 0.5,-0.5 0.1,-0.8 -0.7,-1.3 -1,-1.9 -0.2,-0.1 -0.3,-0.3 -0.5,-0.5 0,-0.2 0,-0.3 0,-0.5 -0.2,-0.1 -0.3,-0.3 -0.5,-0.5 0,-0.3 0,-0.6 0,-1 -0.3,-0.5 -0.3,-1 0,-1.4 0,-0.2 0,-0.3 0,-0.5 0.2,-0.1 0.3,-0.3 0.5,-0.5 0.3,-0.3 0.7,-0.2 1,-0.5 0.6,-0.3 0.5,-0.9 0.5,-1.4 -0.2,-0.2 -0.3,-0.3 -0.5,-0.5 -0.2,0 -0.3,0 -0.5,0 -0.1,-0.2 -0.3,-0.3 -0.5,-0.5 -0.2,-0.2 -0.3,-0.3 -0.5,-0.5 0,-0.5 0,-1 0,-1.4 0.2,-0.1 0.3,-0.3 0.5,-0.5 0.3,-0.3 0.7,-0.2 1,-0.5 0,-0.3 0,-0.6 0,-1 -0.3,-0.3 -0.7,-0.2 -1,-0.5 -0.1,0.2 -0.3,0.1 -0.5,-0.1 z"
+ id="path37-5"
+ style="fill:#ffffff" />
diff --git a/docs/vuegen_case_study_earth_microbiome.ipynb b/docs/vuegen_case_study_earth_microbiome.ipynb
index f62ca51..4945c0b 100644
--- a/docs/vuegen_case_study_earth_microbiome.ipynb
+++ b/docs/vuegen_case_study_earth_microbiome.ipynb
@@ -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"
]
},
{
@@ -78,7 +88,7 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
@@ -113,7 +123,7 @@
},
{
"cell_type": "code",
- "execution_count": 28,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -132,7 +142,7 @@
},
{
"cell_type": "code",
- "execution_count": 29,
+ "execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
@@ -160,7 +170,7 @@
},
{
"cell_type": "code",
- "execution_count": 30,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
@@ -234,7 +244,7 @@
},
{
"cell_type": "code",
- "execution_count": 31,
+ "execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
@@ -257,7 +267,7 @@
},
{
"cell_type": "code",
- "execution_count": 32,
+ "execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
@@ -489,7 +499,7 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
@@ -504,7 +514,7 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
@@ -712,7 +722,7 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
@@ -729,7 +739,7 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
@@ -867,7 +877,7 @@
},
{
"cell_type": "code",
- "execution_count": 33,
+ "execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
@@ -896,7 +906,7 @@
},
{
"cell_type": "code",
- "execution_count": 34,
+ "execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
@@ -1146,7 +1156,7 @@
},
{
"cell_type": "code",
- "execution_count": 25,
+ "execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
@@ -1168,7 +1178,7 @@
},
{
"cell_type": "code",
- "execution_count": 26,
+ "execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
@@ -1190,7 +1200,7 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
@@ -1210,7 +1220,7 @@
},
{
"cell_type": "code",
- "execution_count": 28,
+ "execution_count": 27,
"metadata": {},
"outputs": [],
"source": [
@@ -1230,7 +1240,7 @@
},
{
"cell_type": "code",
- "execution_count": 29,
+ "execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
@@ -1247,7 +1257,7 @@
},
{
"cell_type": "code",
- "execution_count": 30,
+ "execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
@@ -1343,7 +1353,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
@@ -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"
]
},
{
@@ -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",
@@ -1414,7 +1447,7 @@
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": 37,
"metadata": {},
"outputs": [],
"source": [
@@ -1440,7 +1473,7 @@
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
@@ -1471,7 +1504,7 @@
},
{
"cell_type": "code",
- "execution_count": 23,
+ "execution_count": 39,
"metadata": {},
"outputs": [],
"source": [
@@ -1528,7 +1561,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
@@ -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"
]
},
{
diff --git a/src/vuegen/quarto_reportview.py b/src/vuegen/quarto_reportview.py
index f7ad6ce..e68be0c 100644
--- a/src/vuegen/quarto_reportview.py
+++ b/src/vuegen/quarto_reportview.py
@@ -172,7 +172,7 @@ def _create_yaml_header(self) -> str:
""",
@@ -218,7 +218,7 @@ def _create_yaml_header(self) -> str:
""",
diff --git a/src/vuegen/utils.py b/src/vuegen/utils.py
index d9b6bbd..356cc11 100644
--- a/src/vuegen/utils.py
+++ b/src/vuegen/utils.py
@@ -738,7 +738,7 @@ def generate_footer() -> str: