Skip to content

Commit 63b35c3

Browse files
sayalaruanosayalaruano
committed
2 parents 68ee76e + 2f451f0 commit 63b35c3

File tree

8 files changed

+2471
-2407
lines changed

8 files changed

+2471
-2407
lines changed

‎.gitignore‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -128,5 +128,5 @@ docs/images/Graphical_abstract/
128128
docs/images/Nfcore_module_figure
129129
docs/presentations/
130130
docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/
131-
docs/vuegen_case_study_earth_microbiome test.ipynb
131+
docs/vuegen_case_study_earth_microbiome_test.ipynb
132132
test.py

‎docs/example_report.md‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
# Vuegen Case Study - View HTML Report
2+
3+
The stable version of the current `html` report generated in the example notebook
4+
using `vuegen` can be viewed at
5+
6+
[multiomics-analytics-group.github.io/vuegen/](https://multiomics-analytics-group.github.io/vuegen/)

‎docs/images/vuegen_classdiagram_noattmeth.png‎

5.38 KB
Loading

‎docs/images/vuegen_logo.svg‎

Lines changed: 2367 additions & 2374 deletions
Loading

‎docs/index.md‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,14 @@
1414
vuegen_demo
1515
```
1616

17+
```{toctree}
18+
:maxdepth: 1
19+
:caption: Building a report
20+
21+
vuegen_case_study_earth_microbiome
22+
example_report
23+
```
24+
1725
```{toctree}
1826
:maxdepth: 2
1927
:caption: Modules

‎docs/vuegen_case_study_earth_microbiome.ipynb‎

Lines changed: 86 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -65,8 +65,18 @@
6565
"metadata": {},
6666
"outputs": [],
6767
"source": [
68-
"# Install required libraries\n",
69-
"%pip install vuegen cartopy seaborn biom-format"
68+
"# Vuegen library \n",
69+
"%pip install vuegen"
70+
]
71+
},
72+
{
73+
"cell_type": "code",
74+
"execution_count": null,
75+
"metadata": {},
76+
"outputs": [],
77+
"source": [
78+
"# Libraries for the notebook\n",
79+
"%pip install cartopy seaborn biom-format"
7080
]
7181
},
7282
{
@@ -78,7 +88,7 @@
7888
},
7989
{
8090
"cell_type": "code",
81-
"execution_count": 27,
91+
"execution_count": 1,
8292
"metadata": {},
8393
"outputs": [],
8494
"source": [
@@ -113,7 +123,7 @@
113123
},
114124
{
115125
"cell_type": "code",
116-
"execution_count": 28,
126+
"execution_count": 2,
117127
"metadata": {},
118128
"outputs": [],
119129
"source": [
@@ -132,7 +142,7 @@
132142
},
133143
{
134144
"cell_type": "code",
135-
"execution_count": 29,
145+
"execution_count": 3,
136146
"metadata": {},
137147
"outputs": [],
138148
"source": [
@@ -160,7 +170,7 @@
160170
},
161171
{
162172
"cell_type": "code",
163-
"execution_count": 30,
173+
"execution_count": 4,
164174
"metadata": {},
165175
"outputs": [],
166176
"source": [
@@ -234,7 +244,7 @@
234244
},
235245
{
236246
"cell_type": "code",
237-
"execution_count": 31,
247+
"execution_count": 5,
238248
"metadata": {},
239249
"outputs": [],
240250
"source": [
@@ -257,7 +267,7 @@
257267
},
258268
{
259269
"cell_type": "code",
260-
"execution_count": 32,
270+
"execution_count": 6,
261271
"metadata": {},
262272
"outputs": [],
263273
"source": [
@@ -489,7 +499,7 @@
489499
},
490500
{
491501
"cell_type": "code",
492-
"execution_count": 11,
502+
"execution_count": 10,
493503
"metadata": {},
494504
"outputs": [],
495505
"source": [
@@ -504,7 +514,7 @@
504514
},
505515
{
506516
"cell_type": "code",
507-
"execution_count": 12,
517+
"execution_count": 11,
508518
"metadata": {},
509519
"outputs": [],
510520
"source": [
@@ -712,7 +722,7 @@
712722
},
713723
{
714724
"cell_type": "code",
715-
"execution_count": 15,
725+
"execution_count": 14,
716726
"metadata": {},
717727
"outputs": [],
718728
"source": [
@@ -729,7 +739,7 @@
729739
},
730740
{
731741
"cell_type": "code",
732-
"execution_count": 16,
742+
"execution_count": 15,
733743
"metadata": {},
734744
"outputs": [],
735745
"source": [
@@ -867,7 +877,7 @@
867877
},
868878
{
869879
"cell_type": "code",
870-
"execution_count": 33,
880+
"execution_count": 18,
871881
"metadata": {},
872882
"outputs": [],
873883
"source": [
@@ -896,7 +906,7 @@
896906
},
897907
{
898908
"cell_type": "code",
899-
"execution_count": 34,
909+
"execution_count": 19,
900910
"metadata": {},
901911
"outputs": [],
902912
"source": [
@@ -1146,7 +1156,7 @@
11461156
},
11471157
{
11481158
"cell_type": "code",
1149-
"execution_count": 25,
1159+
"execution_count": 24,
11501160
"metadata": {},
11511161
"outputs": [],
11521162
"source": [
@@ -1168,7 +1178,7 @@
11681178
},
11691179
{
11701180
"cell_type": "code",
1171-
"execution_count": 26,
1181+
"execution_count": 25,
11721182
"metadata": {},
11731183
"outputs": [],
11741184
"source": [
@@ -1190,7 +1200,7 @@
11901200
},
11911201
{
11921202
"cell_type": "code",
1193-
"execution_count": 27,
1203+
"execution_count": 26,
11941204
"metadata": {},
11951205
"outputs": [],
11961206
"source": [
@@ -1210,7 +1220,7 @@
12101220
},
12111221
{
12121222
"cell_type": "code",
1213-
"execution_count": 28,
1223+
"execution_count": 27,
12141224
"metadata": {},
12151225
"outputs": [],
12161226
"source": [
@@ -1230,7 +1240,7 @@
12301240
},
12311241
{
12321242
"cell_type": "code",
1233-
"execution_count": 29,
1243+
"execution_count": 28,
12341244
"metadata": {},
12351245
"outputs": [],
12361246
"source": [
@@ -1247,7 +1257,7 @@
12471257
},
12481258
{
12491259
"cell_type": "code",
1250-
"execution_count": 30,
1260+
"execution_count": 29,
12511261
"metadata": {},
12521262
"outputs": [],
12531263
"source": [
@@ -1343,7 +1353,7 @@
13431353
},
13441354
{
13451355
"cell_type": "code",
1346-
"execution_count": null,
1356+
"execution_count": 32,
13471357
"metadata": {},
13481358
"outputs": [],
13491359
"source": [
@@ -1355,7 +1365,30 @@
13551365
"cell_type": "markdown",
13561366
"metadata": {},
13571367
"source": [
1358-
"### 4.2. HTML report"
1368+
"### 4.2. Revealjs report"
1369+
]
1370+
},
1371+
{
1372+
"cell_type": "code",
1373+
"execution_count": 33,
1374+
"metadata": {},
1375+
"outputs": [],
1376+
"source": [
1377+
"# report_type = \"revealjs\"\n",
1378+
"# report_name = \"Earth_microbiome_vuegen_demo_notebook_dir\"\n",
1379+
"\n",
1380+
"# Initialize logger\n",
1381+
"# logger = get_logger(f\"{report_type}_report_{report_name}\")\n",
1382+
"\n",
1383+
"# Generate the report\n",
1384+
"# report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = logger)"
1385+
]
1386+
},
1387+
{
1388+
"cell_type": "markdown",
1389+
"metadata": {},
1390+
"source": [
1391+
"### 4.3. HTML report"
13591392
]
13601393
},
13611394
{
@@ -1391,11 +1424,11 @@
13911424
},
13921425
{
13931426
"cell_type": "code",
1394-
"execution_count": 20,
1427+
"execution_count": 36,
13951428
"metadata": {},
13961429
"outputs": [],
13971430
"source": [
1398-
"empo_logo_path = os.path.join(base_output_dir, \"emp_logo.png\")\n",
1431+
"empo_logo_path = \"https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg\"\n",
13991432
"\n",
14001433
"# Load the YAML file\n",
14011434
"config_path = os.path.join(base_output_dir, \"Earth_microbiome_vuegen_demo_notebook_config.yaml\")\n",
@@ -1414,7 +1447,7 @@
14141447
},
14151448
{
14161449
"cell_type": "code",
1417-
"execution_count": 21,
1450+
"execution_count": 37,
14181451
"metadata": {},
14191452
"outputs": [],
14201453
"source": [
@@ -1440,7 +1473,7 @@
14401473
},
14411474
{
14421475
"cell_type": "code",
1443-
"execution_count": 22,
1476+
"execution_count": 38,
14441477
"metadata": {},
14451478
"outputs": [],
14461479
"source": [
@@ -1471,7 +1504,7 @@
14711504
},
14721505
{
14731506
"cell_type": "code",
1474-
"execution_count": 23,
1507+
"execution_count": 39,
14751508
"metadata": {},
14761509
"outputs": [],
14771510
"source": [
@@ -1528,7 +1561,7 @@
15281561
},
15291562
{
15301563
"cell_type": "code",
1531-
"execution_count": null,
1564+
"execution_count": 41,
15321565
"metadata": {},
15331566
"outputs": [],
15341567
"source": [
@@ -1540,7 +1573,31 @@
15401573
"cell_type": "markdown",
15411574
"metadata": {},
15421575
"source": [
1543-
"### 5.6. HTML report with the extended configuration file"
1576+
"### 5.6. Revealjs report with the extended configuration file"
1577+
]
1578+
},
1579+
{
1580+
"cell_type": "code",
1581+
"execution_count": 42,
1582+
"metadata": {},
1583+
"outputs": [],
1584+
"source": [
1585+
"# Test the changes by generarating the report from the modified YAML file\n",
1586+
"# report_type = \"revealjs\"\n",
1587+
"# report_name = \"Earth_microbiome_vuegen_demo_notebook_config_extended\"\n",
1588+
"\n",
1589+
"# Initialize logger\n",
1590+
"# logger = get_logger(f\"{report_type}_report_{report_name}\")\n",
1591+
"\n",
1592+
"# Generate the report\n",
1593+
"# report_generator.get_report(config_path = config_path, report_type = report_type, logger = logger)"
1594+
]
1595+
},
1596+
{
1597+
"cell_type": "markdown",
1598+
"metadata": {},
1599+
"source": [
1600+
"### 5.7. HTML report with the extended configuration file"
15441601
]
15451602
},
15461603
{

‎src/vuegen/quarto_reportview.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -172,7 +172,7 @@ def _create_yaml_header(self) -> str:
172172
<footer class="footer">
173173
This report was generated with
174174
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
175-
<img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
175+
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
176176
</a>
177177
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
178178
</footer>""",
@@ -218,7 +218,7 @@ def _create_yaml_header(self) -> str:
218218
<footer class="footer">
219219
This report was generated with
220220
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
221-
<img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
221+
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
222222
</a>
223223
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
224224
</footer>""",

‎src/vuegen/utils.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -738,7 +738,7 @@ def generate_footer() -> str:
738738
<footer class="footer">
739739
This report was generated with
740740
<a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
741-
<img src="../../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
741+
<img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
742742
</a>
743743
| © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">
744744
Multiomics Network Analytics Group (MoNA)

0 commit comments

Comments
 (0)